diff --git a/tools/moltemplate/common/graphene.lt b/tools/moltemplate/common/graphene.lt deleted file mode 100644 index 4a17862fc3..0000000000 --- a/tools/moltemplate/common/graphene.lt +++ /dev/null @@ -1,106 +0,0 @@ -# This file contains a unit cell for building graphene and nanotubes -# -# -# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any -# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") -# Surfaces constructed with this unit cell can be flat or curved into tubes. -# The distance between nearest-neighbor carbon atoms (ie the length of a -# carbon-carbon bond) is equal to "d" which I set to 1.420 Angstroms. -# -# d = length of each hexagon's side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms -# -# Consequently, the Lattice-cell vectors for singe-layer graphene are: -# (2.4595121467478, 0, 0) (aligned with X axis) -# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) -# So, to build a sheet of graphite, you could use: -# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) - - - - -Graphene { - - 2AtomCellAlignX - { - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 - $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 - } - } - - # Now define properties of the Carbon graphene atom - - write_once("In Init") { - pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 - } - - write_once("Data Masses") { - @atom:C 12.0 - } - - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 - - # These Lennard-Jones parameters come from - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - - # Define a group consisting of only carbon atoms in graphene molecules - group Cgraphene type @atom:C - } - - # Notice that the two atoms in the unit-cell above lie in the XY plane. - # (Their z-coordinate is zero). It's also useful to have a version of - # this object which lies in the XZ plan. So we define this below: - - 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) - -} # Graphene - - - - - - - - - - -# ------------ Graphite ----------- -# -# Note: For graphite: sheets stacked in the Z direction are separated by a -# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction -# by a distance of d (1.42 Angstroms). To add additional graphene layers -# you could use: -# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet2[*][*].move(0, 1.42, 3.35) -# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet3[*][*].move(0, -1.42, 6.70) -# etc... -# However, to build a thick sheet of graphite, it would -# be more efficient to use a 4-atom unit cell: -# -#Graphene { -# GraphiteCell { -# # atomID molID atomType charge x y z -# write("Data Atoms") { -# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 -# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 -# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 -# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 -# } -# } # GraphiteCell -#} -# -# Then you could create a thick sheet of graphite this way: -# -# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# [5].move(0,0,6.70) diff --git a/tools/moltemplate/common/images/graphene_unit_cell.jpg b/tools/moltemplate/common/images/graphene_unit_cell.jpg deleted file mode 100644 index 12dbf8fca2..0000000000 Binary files a/tools/moltemplate/common/images/graphene_unit_cell.jpg and /dev/null differ diff --git a/tools/moltemplate/common/images/ice_rect8_unitcell.png b/tools/moltemplate/common/images/ice_rect8_unitcell.png deleted file mode 100644 index 5bd6057e1e..0000000000 Binary files a/tools/moltemplate/common/images/ice_rect8_unitcell.png and /dev/null differ diff --git a/tools/moltemplate/common/images/spce_ball_and_stick.jpg b/tools/moltemplate/common/images/spce_ball_and_stick.jpg deleted file mode 100644 index 60aaf90b95..0000000000 Binary files a/tools/moltemplate/common/images/spce_ball_and_stick.jpg and /dev/null differ diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt deleted file mode 100644 index 2b550b6309..0000000000 --- a/tools/moltemplate/common/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/common/spce_ice_rect8.lt b/tools/moltemplate/common/spce_ice_rect8.lt deleted file mode 100644 index ccfd2f18c6..0000000000 --- a/tools/moltemplate/common/spce_ice_rect8.lt +++ /dev/null @@ -1,57 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 8 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect8 { - - # Create a 3-dimensional array of 8 water molecules - - wat = new SPCE[2][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 - } -} # IceRect8 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/common/tip3p_attempts/README.TXT b/tools/moltemplate/common/tip3p_attempts/README.TXT deleted file mode 100644 index 13a2626d42..0000000000 --- a/tools/moltemplate/common/tip3p_attempts/README.TXT +++ /dev/null @@ -1,13 +0,0 @@ -This directory contains two LT files corresponding to -different versions of TIP3P: - -tip3pcharmm.lt # The implementation of TIP3P used by CHARMM (I think). -tip3p2004.lt # The newer Price & Brooks, J. Chem Phys 2004 model - # which uses long-range coulombics - -I have not tested these files so I moved them here. -(If you have tested these files, and they work, or if you have other comments -or suggestions, feel free to email me at jewett.aij at gmail dot com.) - -Andrew -2012-10-20 diff --git a/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt b/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt deleted file mode 100644 index f04a161b35..0000000000 --- a/tools/moltemplate/common/tip3p_attempts/tip3p2004.lt +++ /dev/null @@ -1,88 +0,0 @@ -# file "tip3p2004.lt" -# -# H1 H2 -# \ / -# O -# -# I think this is the TIP3P water described in the paper by -# Daniel J. Price and Charles L. Brooks III -# J. Chem. Phys., 121(20): 10096 (2004) -# Specifically I think it refers to the "Model B" version of long-range TIP3P -# described in the 3rd-to-last column of "Table I", on p.10099. - -TIP3P2004 { - - write_once("In Init") { - # -- Default styles (for solo "TIP3P2004" water) -- - units real - atom_style full - - pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.830 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.415 0.756950327 0.00000 0.5858822766 - $atom:H2 $mol:. @atom:H 0.415 -0.756950327 0.00000 0.5858822766 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 450.0 0.9572 - angle_coeff @angle:HOH harmonic 55.0 104.52 - - ######################################################################### - #### There are two choices for for the O-O interactions - ######################################################################### - #### O-O nonbonded interactions - # For the 1983 Jorgensen version of TIP3P use: - # pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 - # For the 2004 Price & Brooks version of TIP3P use: - pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188 - ######################################################################### - #### There are three choices for for the O-H and H-H interactions - ######################################################################### - #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic - ######################################################################### - #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, - #### If you want to use this, uncomment the following two lines: - # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric - ######################################################################### - #### 3) The original Jorgensen 1983 parameterization has no OH or HH - # lennard-jones interactions. For this behavior, uncomment these lines: - # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 - # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 - ######################################################################### - - # Define a group for the tip3p water molecules: - group tip3p type @atom:O @atom:H - - # Optional: Constrain the angles and distances. - # (Most implementations use this, but it is optional.) - fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - - } - -} # "TIP3P2004" water molecule type - diff --git a/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt b/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt deleted file mode 100644 index 80ea280fa5..0000000000 --- a/tools/moltemplate/common/tip3p_attempts/tip3pcharmm.lt +++ /dev/null @@ -1,91 +0,0 @@ -# file "tip3p_charmm.lt" -# -# H1 H2 -# \ / -# O -# -# I think this is the TIP3P water model used by CHARMM (and probably AMBER) -# It is (mostly) based on this paper: -# Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem Phys, 79, 926 (1983) - -TIP3Pcharmm { - - write_once("In Init") { - # -- Default styles (for solo "TIP3Pcharmm" water) -- - units real - atom_style full - - # I'm not sure exactly which cutoffs distances are traditionally used in - # the TIP3P water model used by CHARMM. - # (See the Price JCP 2004 paper for a review.) - # pair_style hybrid lj/charmm/coul/charmm 7.5 8.0 10.0 10.5 - # Try this instead: - pair_style hybrid lj/charmm/coul/charmm 10.0 10.5 10.0 10.5 - - bond_style hybrid harmonic - angle_style hybrid harmonic - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.834 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.417 0.756950327 0.00000 0.5858822766 - $atom:H2 $mol:. @atom:H 0.417 -0.756950327 0.00000 0.5858822766 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 450.0 0.9572 - angle_coeff @angle:HOH harmonic 55.0 104.52 - - ######################################################################### - #### There are two choices for for the O-O interactions - ######################################################################### - #### O-O nonbonded interactions - # For the 1983 Jorgensen version of TIP3P use: - pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.1521 3.1507 - # For the 2004 Price & Brooks version of TIP3P use: - # pair_coeff @atom:O @atom:O lj/charmm/coul/charmm 0.102 3.188 - ######################################################################### - #### There are three choices for for the O-H and H-H interactions - ######################################################################### - #### 1) CHARMM uses an arithmetic mixing-rule for the O-H sigma parameter - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.7753 #arithmetic - ######################################################################### - #### 2) OPLS-AA uses geometric a mixing-fule for the O-H sigma parameter, - #### If you want to use this, uncomment the following two lines: - # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.0460 0.4000 - # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.0836 1.1226 #geometric - ######################################################################### - #### 3) The original Jorgensen 1983 parameterization has no OH or HH - # lennard-jones interactions. For this behavior, uncomment these lines: - # pair_coeff @atom:H @atom:H lj/charmm/coul/charmm 0.00 0.4000 - # pair_coeff @atom:O @atom:H lj/charmm/coul/charmm 0.00 1.7753 - ######################################################################### - - # Define a group for the tip3p water molecules: - group tip3p type @atom:O @atom:H - - # Optional: Constrain the angles and distances. - # (Most implementations use this, but it is optional.) - fix fSHAKE tip3p shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - - } - -} # "TIP3Pcharmm" water molecule type - diff --git a/tools/moltemplate/common/trappe1998.lt b/tools/moltemplate/common/trappe1998.lt deleted file mode 100644 index 9bcc80cb1c..0000000000 --- a/tools/moltemplate/common/trappe1998.lt +++ /dev/null @@ -1,50 +0,0 @@ -# This file stores complete LAMMPS data for the TraPPE model of saturated -# hydrocarbon chains. In this "united-atom" model, each methyl group is -# represented by a single atom. Forces between "atoms" are taken from the -# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) - -TraPPE { - - write_once("In Init") { - # -- Default styles for "TraPPE" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style none - pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - @atom:CH4 16.3307 - } - - write_once("Data Angles By Type") { - @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated - } - - write_once("Data Dihedrals By Type") { - @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated - } - - write_once("In Settings") { - pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 - pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 - pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 - bond_coeff @bond:saturated harmonic 120.0 1.54 - angle_coeff @angle:backbone harmonic 62.0022 114 - dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 - } - - write_once("In Settings") { - group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 - } - -} # class TraPPE - diff --git a/tools/moltemplate/common/watmw.lt b/tools/moltemplate/common/watmw.lt deleted file mode 100644 index c7aaecebbc..0000000000 --- a/tools/moltemplate/common/watmw.lt +++ /dev/null @@ -1,54 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT deleted file mode 100644 index 09abbc4b2a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README.TXT +++ /dev/null @@ -1,70 +0,0 @@ - This example shows how to put a protein (inclusion) in a - lipid bilayer mixture composed of two different lipids (DPPC and DLPC). - The DPPC lipid model is described here: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) - (The DLPC model is a truncated version of DPPC. Modifications discussed below.) - The protein model is described here: - G. Bellesia, AI Jewett, and J-E Shea, - Protein Science, Vol19 141-154 (2010) - ---- PREREQUISITES: --- - -1) This example requires the "dihedral_style fourier", which is currently -in the USER-MISC package. Build LAMMPS with this package enabled using - make yes-user-misc -before compiling LAMMPS. -(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) - -2) This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then - a) download the "additional_lammps_code" from - http://moltemplate.org (upper-left corner menu) - b) unpack it - c) copy the .cpp and .h files to the src folding of your lammps installation. - d) (re)compile LAMMPS. - - ------ Details -------- - -This example contains a coarse-grained model of a 4-helix bundle protein -inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). - - -- Protein Model: -- - -The coarse-grained protein is described in: - G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -Here we use the "AUF2" model described in that paper. -(The hydrophobic beads face outwards.) - - -- Memebrane Model: -- - -The DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -The bending stiffness of each lipid has been increased to compensate -for the additional disorder resulting from mixing two different types -of lipids together. (Otherwise pores appear.) -Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models -have not been carefully parameterized to reproduce the correct behavior in -a lipid bilayer mixture. - - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh deleted file mode 100755 index 9598e3b08d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) - -#or - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#or -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh deleted file mode 100755 index abf2fce64b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg deleted file mode 100644 index 246ee54625..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index cf5ef4faf5..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,2611 +0,0 @@ -PSF - 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diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg deleted file mode 100644 index fdbb446eed..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg deleted file mode 100644 index 142f3f706f..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_no_pbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg deleted file mode 100644 index 5d4b15b291..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=0ps_top_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg deleted file mode 100644 index 285389039d..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/images/membrane+protein_t=5000ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index a5df81056d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,254 +0,0 @@ -# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle (or a 4-strand beta-barrel). -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 - $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 - $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 - $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 - $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 - $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 - $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 - $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 - $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 - $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 - $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 - $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 - $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 - $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 - $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 - $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 - $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 - $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - - # ----- Now build a larger molecule using A16 and T3 ------- - - # Create a 4-Helix bundle. - # In this version, the hydrophobic beads are poing outward. - # I oriented them this way because I want to place this protein in a membrane. - # (There is another file in this directory containing alternate version - # of this same molecule with the hydrophobic beads pointing inward.) - - 4HelixInsideOut { - helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) - - turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) - turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) - turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOut - - - # -------- Minor coordinates adjustment: ----------- - - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) - - 4HelixInsideOut.scale(0.9166666666666666) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - - - # -------------- Force-Field Parameters ------------ - - # Units and force-field styles for this protein model - # (These can be overridden later.) - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - # --- Distance Units --- - # In this version of the model, sigma (the bond-length - # and particle diameter) is rounded to 5.5 Angstroms. - # - # --- Energy & Temperature Units --- - # In this protein model, "epsilon" represents the free energy - # bonus for bringing two hydrophobic amino acids together. - # Here I choose to set epsilon to 1.806551818181818 kCal/mole. - # This value was chosen so that a temperature of 300 Kelvin lies at - # 0.33 epsilon, which is the unfolding temperature of the marginally stable - # "ASF1" protein model from the Bellesia et al 2010 paper. - # This choice insures that both the "ASF1" model from that paper, - # as well as the much more stable "AUF2" protein we use here (which - # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, - # in the bulk at least. (However it's not clear that these energy - # parameters will work well for a protein in membrane. Perhaps I'll - # run some tests and fine tune these parameters for this scenario.) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - } - - # The exact value of the bond_coeff does not matter too much as long as - # it is "stiff enough". Here I use a softer bond spring than the one - # used in the paper so that I can increase the time step. - # I also use a relatively soft spring to constrain the bond angles. - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 - } - - - - # We use the same bond-angle forces whenever - # there are 3 consecutively-bonded atoms: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # angle_coeff angleType anglestylename k theta0 - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 100.0 105.0 - } - - - - - # Dihedral interactions are also determined by atom-type name in this case. - # I chose atoms whose type-names begin with "t" to be "turn" atoms. - # Atoms whose type-names begin with "s" could be either helices or sheets. - # (In this case, helices. In this example, we use the @dihedral:delta65_0 - # parameters. This corresponds to the "AUF2" model from the - # Bellesia et. al 2010 paper.) - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * - - # If "tN" (turn) atoms are present, use the @dihedral:turn parameters - - @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * - } - - - # From the Bellesia et al 2010 paper: - # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) - # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) - # - # General formula used for "dihedral_style fourier": - # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] - # - # Syntax: - # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # --- Mass Units --- - # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): - write_once("Data Masses") { - @atom:1beadProtSci2010/sH 100.0 - @atom:1beadProtSci2010/sL 100.0 - @atom:1beadProtSci2010/tN 100.0 - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt deleted file mode 100644 index e6e6bced70..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt +++ /dev/null @@ -1,225 +0,0 @@ -### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## -### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## -# -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) - -import "1beadProtSci2010.lt" - -# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. - - -1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier - # This way we don't have to start from scratch. We can - # use all the atom types and angle settings defined earlier - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 - $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 - $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 - $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 - $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 - $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 - $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 - $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 - $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 - $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 - $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 - $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 - $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 - $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 - $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 - $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - # ----- Now build larger molecules using B16 and T3 ------- - - - 4SheetBarrel { - sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) - sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) - sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) - sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # Below I define several alternate conformations of the"4HelixBundleInsideOut" - # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. - - 4HelixBundle { - helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - - turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) - turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) - turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) - - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixBundle - - - - - # --- alternate conformations (same molecule) ---- - - # In the following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixBundleLoose { - - helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # In following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixInsideOutLoose { - helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) - turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) - turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOutLoose - - - - - # In the following version, the 4 helices are arranged next to each other, - # side-by-side, in a planar conformation (instead of a compact bundle). - - 4HelixPlanar { - helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) - helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) - helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) - helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) - turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) - turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixPlanar - - - # -------- Minor coordinates adjustment: ----------- - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) - - 4SheetBarrel.scale(0.9166666666666666) - 4HelixBundle.scale(0.9166666666666666) - 4HelixBundleLoose.scale(0.9166666666666666) - 4HelixInsideOutLoose.scale(0.9166666666666666) - 4HelixPlanar.scale(0.9166666666666666) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index 3b39048f7e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,198 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# A truncated version of this lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer mixture. -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - - #angle_style hybrid cosine/delta # <- used in the original article - angle_style hybrid harmonic # <- prevents unphysical acute angle turns - # Explanation: - # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - # angle_style harmonic: U(theta) = k*(theta-theta0)^2 - - dihedral_style none - improper_style none - pair_style hybrid table linear 1130 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - communicate multi # <- perhaps unnecessary - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles and properties shared by all lipid types: - - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - @atom:head 200.0 #<- Default head type. We may override it later. - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 - angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps - } - # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper - # to attempt to compensate for the fact that here we are using a lipid - # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal - # of disorder into the bilayer which would not be present in a DPPC bilayer. - # This causes pores to form. Increasing the angle stiffness prevents this.) - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction of head beads which all other beads is given by: - # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), - - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - } # write_once("In Settings") - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py deleted file mode 100755 index 1eb97e6454..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -# The previous version included the repulsive core term -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) -# We don't want to do that. Instead compute the core repulsion using a -# different pair_style and add the attractive term on top of it using the table. -# This way it the core repulsion acts as a default interaction with other atom -# types (using the new repulsive mixing rules). - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index 32147e444a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt deleted file mode 100644 index 51a67b6d9f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/system.lt +++ /dev/null @@ -1,207 +0,0 @@ -# Description: - -# This example shows how to put a protein (inclusion) in a -# lipid bilayer mixture composed of two different lipids (DPPC and DLPC). -# The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The protein model is described here: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to -# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 - -# Note: -# This example may require additional features to be added to LAMMPS. -# If LAMMPS complains about an "Invalid pair_style", then copy the code -# in the "additional_lammps_code" directory into your LAMMPS "src" directory -# and recompile LAMMPS. - - - -import "CGLipidBr2005.lt" - -using namespace CGLipidBr2005 - -# The "= new random" syntax chooses one of several molecules at random - -lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed - [13].move(7.5, 0, 0) - [15].move(3.75, 6.49519, 0) # <-- hexagonal lattice - [2].rot(180, 1, 0, 0) # <-- 2 monolayers - -# Move all the lipds up to the center of the box - -lipids[*][*][*].move(0,0,75.0) - - - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. (Check by visualising in VMD.) - - -write_once("Data Boundary") { - 0 97.5 xlo xhi - 0 97.42785792 ylo yhi - 0 150.0 zlo zhi -} - - -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 15 rows (each row is aligned with the x-axis) -# 13 columns (aligned at a 60 degree angle from the x axis) -# The lattice spacing is 7.5 Angstroms. -# When wrapped onto a rectangular box, the dimensions of the system are: -# 13 * 7.5 Angstroms in the X direction -# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction - - - - - - - -# ------------------- protein inclusion --------------------- - -import "1beadProtSci2010.lt" - -using namespace 1beadProtSci2010 - -protein = new 4HelixInsideOut - -protein.move(45.0, 25.98076211, 75.0) - - -# Delete a hole in the membrane to create space for the protein. - -delete lipids[4][2][*] -delete lipids[6][2][*] -delete lipids[3-6][3][*] -delete lipids[3-5][4][*] -delete lipids[2-5][5][*] -delete lipids[2][6][*] -delete lipids[4][6][*] - -# Note: All atom types must include the full path (the name of -# the namespace which defined them as well as the atom type name). -# (This is because we are no longer inside that namespace.) - - -write_once("In Settings") { - - # ----------------------------------------------------------- - # -------- interactions between protein and lipids ---------- - # ----------------------------------------------------------- - - # Interactions between the protein and lipid atoms are usually - # determined by mixing rules. (However this is not possible some - # for atoms, such as the "int" atoms in the lipid model which - # interact using -1/r^2 attraction.) Mixing rules do not make - # sense for these atoms so we must explicitly define their - # interaction with all other atoms. - - # We want the hydrophobic interactions between hydrophobic residues in - # the protein and beads the interior of the lipid to be energetically - # similar to the attractive interactions between the lipid tails. - # - # Note: I made the width of the outward-facing protein beads slightly larger - # ("12.5") whenever they interact with the "tail" beads in each lipid - # (in order to make the protein wider there). - # This hopefully relieves some of the internal negative pressure in the center - # of the bilayer which can otherwise rip apart the protein or suck it into - # the bilaer. (This is a hack, and I'm not sure if it is necessary. - # For different protein or lipid models, you probably don't need this.) - # - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # To help keep the protein from tilting 90 degrees and burying itself - # within the lipid bilayer, we make the turn regions at either - # end of the protein (strongly) attracted to the head groups - # of the lipid. (In reality, they would probably be attracted - # to the water as well.) - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # All other interactions between proteins and lipids are steric. - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - # ----------------------------------------------------------- - # -------- Modifications to the protein model: -------------- - # ----------------------------------------------------------- - # - # Turn off attraction between the hydrophobic "@atom:sH" beads: - # (These beads are located in the outside of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - - # (Why: These beads are only attracted to - # each other in an aqueous environment) - - # ... and - # Turn ON attraction between the hydrophilic "@atom:sL" beads. - # (These beads are located in the interior of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # Why? - # In reality, polar groups in the interior of trans-membrane - # proteins do form hydrogen bonds with each other. This was - # absent from the original protein model because, in an aqueous - # environment, these groups preferentially interact with the water. - # - # Why is this necessary? - # Shouldn't attraction between lipid tails and the protein create - # an effective force which brings the hydrophilic beads together? - # (similar to the hydrophobic effect, but in reverse?). - # Answer: - # Unlike an aqueous environment (~zero pressure, or +1atm), there is - # a large negative pressure in the interior of some bilayer membrane - # models (such as this one). Without some kind of direct attraction - # between interior residues, the protein will get pulled apart. - # (Perhaps the attractive force I am using is too strong?) - -} - - - - -# Finally, we must combine the two force-field styles which were used for -# the coarse-grained lipid and protein. To do that, we write one last time -# to the "In Init" section. When reading the "Init" section LAMMPS will -# read these commands last and this will override any earlier settings. - -write_once("In Init") { - # -- These styles override earlier settings -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta harmonic - dihedral_style hybrid fourier - improper_style none - pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" -} - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 27268725.7382 -95 1.9 3762612.01167 23764025.6584 -96 1.92 3318314.28383 20739619.609 -97 1.94 2930293.18879 18125675.4316 -98 1.96 2590946.89128 15863086.114 -99 1.98 2293763.15199 13901736.4186 -100 2.0 2033154.33079 12199063.3122 -101 2.02 1804318.68586 10718858.1296 -102 2.04 1603123.57305 9430268.02169 -103 2.06 1426006.91783 8306962.01537 -104 2.08 1269893.96121 7326433.30293 -105 2.1 1132126.79514 6469414.48445 -106 2.12 1010404.62602 5719386.63441 -107 2.14 902733.052344 5062166.44376 -108 2.16 807380.928986 4485558.44681 -109 2.18 722843.627253 3979061.59742 -110 2.2 647811.695319 3533621.30686 -111 2.22 581144.085827 3141419.57242 -112 2.24 521845.251959 2795697.07302 -113 2.26 469045.525153 2490602.13576 -114 2.28 421984.280794 2221062.32522 -115 2.3 379995.475978 1982675.10836 -116 2.32 342495.208369 1771614.62868 -117 2.34 308970.999537 1584552.10475 -118 2.36 278972.551763 1418587.76828 -119 2.38 252103.765513 1271192.59046 -120 2.4 228015.837009 1140158.32224 -121 2.42 206401.282366 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-0.00354788564052 -0.0199492167196 -1117 22.34 -0.0031494369093 -0.0198956883597 -1118 22.36 -0.00275205683071 -0.0198423513132 -1119 22.38 -0.00235574158704 -0.0197892047262 -1120 22.4 -0.00196048737759 -0.0197362477497 -1121 22.42 -0.00156629041861 -0.0196834795391 -1122 22.44 -0.00117314694319 -0.0196308992543 -1123 22.46 -0.000781053201174 -0.0195785060596 -1124 22.48 -0.000390005459079 -0.019526299124 -1125 22.5 0.0 -0.0194742776206 -1126 22.52 0.0 0.0 -1127 22.54 0.0 0.0 -1128 22.56 0.0 0.0 -1129 22.58 0.0 0.0 -1130 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min deleted file mode 100644 index fb2d3ddd87..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.min +++ /dev/null @@ -1,35 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. - - - -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt deleted file mode 100644 index f5f117ece1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt +++ /dev/null @@ -1,60 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -#minimize 1.0e-5 1.0e-7 500 2000 - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - - -# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon -# (for the "epsilon" used by the coarse-grained lipid), and -# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein) -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -run 10000000 - -write_restart system_after_npt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt deleted file mode 100644 index 2ee9ae0199..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt +++ /dev/null @@ -1,67 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Until then, try "read_dump", "dump2data.py", or "restart2data". - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -#restart 500000 - -run 10000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT deleted file mode 100644 index 295af3fd16..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README.TXT +++ /dev/null @@ -1,33 +0,0 @@ -Note: - This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then copy the code -in the "additional_lammps_code" directory into your LAMMPS "src" directory -and recompile LAMMPS. - ------ Description -------- - -This example contains an implementation of the DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -parameterized to reproduce the correct behavior in a lipid bilayer mixture. - - -------------- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh deleted file mode 100755 index 9598e3b08d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension) - -#or - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#or -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh deleted file mode 100755 index abf2fce64b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_setup.sh +++ /dev/null @@ -1,28 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg deleted file mode 100644 index 637f2f1c7a..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DLPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg deleted file mode 100644 index 14f1a1ed2c..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg deleted file mode 100644 index 757abe2684..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg deleted file mode 100644 index 2322449c1d..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg deleted file mode 100644 index 57e093023d..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/images/DPPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt deleted file mode 100644 index c0478f1425..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005Orig.lt +++ /dev/null @@ -1,191 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# --- DLPC lipids --- -# A truncated version of the DPPC lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer/mixture. -# (You may need to stiffen the bond-angle forces to make it behave correctly, -# but I did not do this here.) -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. -# -# -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta - dihedral_style none - improper_style none - pair_style hybrid table linear 1001 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - communicate multi # <- perhaps unnecessary - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles shared by all lipid types - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - @atom:head 200.0 #<- Default head type. We may override it later. - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - #angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps - } - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction of head beads which all other beads is given by: - # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), - - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - } # write_once("In Settings") - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py deleted file mode 100755 index 1eb97e6454..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -# The previous version included the repulsive core term -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) -# We don't want to do that. Instead compute the core repulsion using a -# different pair_style and add the attractive term on top of it using the table. -# This way it the core repulsion acts as a default interaction with other atom -# types (using the new repulsive mixing rules). - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index 32147e444a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt deleted file mode 100644 index c556233c0d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/system.lt +++ /dev/null @@ -1,94 +0,0 @@ -# Description: - -# This constructs a bilayer constructed from coarse-grained DPPC lipids -# (implicit solvent). The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# -# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture -# in the "membrane+protein" and "vesicle" examples. - - - - - - -import "CGLipidBr2005Orig.lt" - -using namespace CGLipidBr2005 - -lipids = new DPPC [32].move(7.5, 0, 0) - [37].move(3.75, 6.49519, 0) - [2].rot(180, 1, 0, 0) - - -# Move the lipds up to the center of the box -lipids[*][*][*].move(0,0,75.0) - - -# Although this patch of lipids is not square or rectangular, (it looks -# like a parallelogram), this is no longer the case after rectangular -# periodic boundary conditions are applied. We apply them below: -# width: 240 = 32*7.5 -# height: 240.322 = 37*6.49519 - -write_once("Data Boundary") { - 0 240 xlo xhi - 0 240.322 ylo yhi - 0 150.0 zlo zhi -} - - - - - - - - -# -------------- File ends here. Only comments below.------------------- - -# ------------------------------------ -# ------------- COMMENTS: ------------ -# ------------------------------------ -# -# A note on geometry: -# We want to create a bilayer arranged in a hexagonal lattice consisting of -# 32 rows (each row is aligned with the x-axis) -# 37 columns (aligned at a 60 degree angle from the x axis) -# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5) -# When wrapped onto a rectangular box, the dimensions of the system are: -# 32 * 7.5 Angstroms in the X direction -# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction -# ------------------------------------ -# -# Below I show simple ways to create a lipid bilayer: -# -# 1) If you just want to make lipid bilayer out of DPPC, -# without specifying the location of each lipid, you could use this syntax: -# lipids = new DPPC [32][37][2] # 3-D array -# Later you can load in the coordinates of the lipds from a PDB file. -# Alternately you could also use a 1-dimensional array: -# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2 -# It does not matter as long as the number of lipids is correct. -# Multidimensional arrays are only useful if you plan to apply independent -# coordinate transformations to each row and column and monolayer. See below: -# -# 2) Instead of loading a PDB file later, we can directly specify the location -# of each DPPC lipid in the LT file itself. For lipid bilayers, this is -# easy, because the bilayer structure resembles 2 planar lattices. -# We can use "move" commands to place each lipid, and the "rot" command -# to turn the lipids in one of the monolayers upside down. -# -# lipids = new DPPC [32].move(7.5, 0, 0) -# [37].move(3.75, 6.49519, 0) -# [2].rot(180, 1, 0, 0) -# -# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must -# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345) -# Here "0.5,0.5" are the probabilities for each molecule type, and "12345" -# is an optional random seed. -# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345) -# [32].move(7.5, 0, 0) -# [37].move(3.75, 6.49519, 0) -# [2].rot(180, 1, 0, 0) -# diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 27268725.7382 -95 1.9 3762612.01167 23764025.6584 -96 1.92 3318314.28383 20739619.609 -97 1.94 2930293.18879 18125675.4316 -98 1.96 2590946.89128 15863086.114 -99 1.98 2293763.15199 13901736.4186 -100 2.0 2033154.33079 12199063.3122 -101 2.02 1804318.68586 10718858.1296 -102 2.04 1603123.57305 9430268.02169 -103 2.06 1426006.91783 8306962.01537 -104 2.08 1269893.96121 7326433.30293 -105 2.1 1132126.79514 6469414.48445 -106 2.12 1010404.62602 5719386.63441 -107 2.14 902733.052344 5062166.44376 -108 2.16 807380.928986 4485558.44681 -109 2.18 722843.627253 3979061.59742 -110 2.2 647811.695319 3533621.30686 -111 2.22 581144.085827 3141419.57242 -112 2.24 521845.251959 2795697.07302 -113 2.26 469045.525153 2490602.13576 -114 2.28 421984.280794 2221062.32522 -115 2.3 379995.475978 1982675.10836 -116 2.32 342495.208369 1771614.62868 -117 2.34 308970.999537 1584552.10475 -118 2.36 278972.551763 1418587.76828 -119 2.38 252103.765513 1271192.59046 -120 2.4 228015.837009 1140158.32224 -121 2.42 206401.282366 1023554.60663 -122 2.44 186988.75765 919692.114521 -123 2.46 169538.563484 827090.818108 -124 2.48 153838.739168 744452.651831 -125 2.5 139701.665073 670637.92543 -126 2.52 126961.103835 604644.949624 -127 2.54 115469.620781 545592.416037 -128 2.56 105096.332511 492704.141327 -129 2.58 95724.9397832 445295.843157 -130 2.6 87252.0069441 402763.664479 -131 2.62 79585.4554502 364574.203947 -132 2.64 72643.2434671 330255.845328 -133 2.66 66352.2073932 299391.208536 -134 2.68 60647.0444312 271610.570248 -135 2.7 55469.4181565 246586.123584 -136 2.72 50767.1714483 224026.964698 -137 2.74 46493.633237 203674.709811 -138 2.76 42607.0073083 185299.659567 -139 2.78 39069.8329526 168697.439095 -140 2.8 35848.5085794 153686.051901 -141 2.82 32912.8705664 140103.294183 -142 2.84 30235.8206098 127804.483324 -143 2.86 27792.9956998 116660.460548 -144 2.88 25562.4755962 106555.833042 -145 2.9 23524.5233195 97387.4254387 -146 2.92 21661.3547409 89062.9145204 -147 2.94 19956.9338374 81499.6244039 -148 2.96 18396.7906059 74623.4624292 -149 2.98 16967.8589974 68367.9785194 -150 3.0 15658.3325568 62673.5329856 -151 3.02 14457.5357325 57486.5596649 -152 3.04 13355.809067 52758.912937 -153 3.06 12344.4066925 48447.2886046 -154 3.08 11415.4047444 44512.7098736 -155 3.1 10561.6194689 40920.0707567 -156 3.12 9776.5339459 37637.7301715 -157 3.14 9054.23247117 34637.1508274 -158 3.16 8389.34175838 31892.5777179 -159 3.18 7776.97821258 29380.7516608 -160 3.2 7212.7006167 27080.6538766 -161 3.22 6692.4676457 24973.2780793 -162 3.24 6212.59969004 23041.4269669 -163 3.26 5769.74452856 21269.5303734 -164 3.28 5360.84644195 19643.4826615 -165 3.3 4983.1184041 18150.4972204 -166 3.32 4634.01702836 16778.97618 -167 3.34 4311.21998136 15518.393672 -168 3.36 4012.60560869 14359.191159 -169 3.38 3736.23454428 13292.6835236 -170 3.4 3480.33310029 12310.9747549 -171 3.42 3243.27825585 11406.8822043 -172 3.44 3023.58408279 10573.8684961 -173 3.46 2819.88946345 9805.98028003 -174 3.48 2630.94697101 9097.79310596 -175 3.5 2455.61279669 8444.36177626 -176 3.52 2292.83761972 7841.17560602 -177 3.54 2141.65832756 7284.11808108 -178 3.56 2001.19050257 6769.43046025 -179 3.58 1870.62160083 6293.67891689 -180 3.6 1749.20475558 5853.72485855 -181 3.62 1636.25314534 5446.69810179 -182 3.64 1531.13487237 5069.97261409 -183 3.66 1433.26830277 4721.1445646 -184 3.68 1342.11782445 4398.01245332 -185 3.7 1257.18998347 4098.55911171 -186 3.72 1178.02996319 3820.93539003 -187 3.74 1104.21837425 3563.44536511 -188 3.76 1035.36832639 3324.53291993 -189 3.78 971.122756088 3102.76956138 -190 3.8 911.151986554 2896.84335615 -191 3.82 855.151498616 2705.54887715 -192 3.84 802.83989347 2527.77806329 -193 3.86 753.957029799 2362.51190574 -194 3.88 708.262319576 2208.81288195 -195 3.9 665.533168297 2065.81806693 -196 3.92 625.563546756 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/dev/null @@ -1,28 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -#pair_write 2 2 1001 r 2.6 16.0 test_tail-tail.dat t-t 0 0 -#pair_write 2 3 1001 r 2.6 16.0 test_tail-head.dat t-h 0 0 -#pair_write 1 2 1001 r 2.6 16.0 test_int-tail.dat i-t 0 0 -#pair_write 1 1 2573 r 2.6 16.0 test_int-int.dat i-i 0 0 -#pair_write 1 3 1001 r 2.6 16.0 test_int-head.dat i-h 0 0 -#pair_write 3 3 1001 r 2.6 16.0 test_head-head.dat h-h 0 0 - - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt deleted file mode 100644 index bd86869ab7..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.npt +++ /dev/null @@ -1,57 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example may require additional features and bug fixes for LAMMPS. -# Be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 2) Unpack it -# 3) copy the .cpp and .h files to the src folding of your lammps installation. -# 4) Compile LAMMPS. -# -# (If LAMMPS complains about an "Invalid pair_style" -# then you made a mistake in the instructions above.) -# - -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy - - -# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon -# for the "epsilon" used by the coarse-grained lipid. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. -# Note: We maintain the system system at constant (zero) tention -# using a barostat damping parameter Pdamp=1000 ("0 0 1000") - - -# optional (not sure if this helps): -# balance x uniform y uniform - - -#restart 1000000 - -run 2000000 - -write_restart system_after_npt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt deleted file mode 100644 index 775c074c21..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/run.in.nvt +++ /dev/null @@ -1,53 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Until then, try "read_dump", "dump2data.py", or "restart2data". - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 1000 # time interval for printing out "thermo" data - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -#restart 1000000 - -run 1000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT deleted file mode 100644 index 31abcd66ef..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/README.TXT +++ /dev/null @@ -1,33 +0,0 @@ -# This directory contains examples of how to run a short simulation of a -# coarse-grained protein-like polymer, folding in the presence and absence of -# a chaperone (modeled as an attractive or repulsie spherical shell). -# -# The protein models and the chaperone models are described and used here: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# ...and also here: -# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) -# -# (In the "frustrated+minichaperone" directory, the protein is -# placed outside the chaperone sphere, as opposed to inside.) -# -# -------- REQUIREMENTS: --------- -# 1) These examples require the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) They also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files in each directory. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT deleted file mode 100644 index a52f73ff7b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT +++ /dev/null @@ -1,32 +0,0 @@ -# This directory demonstrates how to run a long simulation of -# the "frustrated" coarse-grained protein confined in a frustrated -# coarse-grained chaperonin (R=6, h=0.475) as described in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# Note: If you want to use a "hydrophilic" chaperone (with h=0.0 -# instead of h=0.475), then replace the word "CHAP_INTERIOR_H0.475" -# (at the end of "system.lt") with "CHAP_INTERIOR_H0" -# -# Because this process takes a long time (even with the help of the chaperone) -# I save the data relatively infrequently. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 9e34246f8e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,86 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 28 !NATOM - 1 1 2 2 0.000000 1.0000 0 - 2 1 1 1 0.000000 1.0000 0 - 3 1 2 2 0.000000 1.0000 0 - 4 1 1 1 0.000000 1.0000 0 - 5 1 2 2 0.000000 1.0000 0 - 6 1 1 1 0.000000 1.0000 0 - 7 1 3 3 0.000000 1.0000 0 - 8 1 3 3 0.000000 1.0000 0 - 9 1 1 1 0.000000 1.0000 0 - 10 1 2 2 0.000000 1.0000 0 - 11 1 1 1 0.000000 1.0000 0 - 12 1 2 2 0.000000 1.0000 0 - 13 1 1 1 0.000000 1.0000 0 - 14 1 2 2 0.000000 1.0000 0 - 15 1 3 3 0.000000 1.0000 0 - 16 1 3 3 0.000000 1.0000 0 - 17 1 3 3 0.000000 1.0000 0 - 18 1 1 1 0.000000 1.0000 0 - 19 1 1 1 0.000000 1.0000 0 - 20 1 2 2 0.000000 1.0000 0 - 21 1 2 2 0.000000 1.0000 0 - 22 1 1 1 0.000000 1.0000 0 - 23 1 1 1 0.000000 1.0000 0 - 24 1 2 2 0.000000 1.0000 0 - 25 1 2 2 0.000000 1.0000 0 - 26 1 1 1 0.000000 1.0000 0 - 27 1 2 2 0.000000 1.0000 0 - 28 2 4 4 0.000000 100.0000 0 - - 26 !NBOND: bonds - 1 2 2 3 3 4 4 5 - 5 6 6 7 7 8 8 9 - 9 10 10 11 11 12 12 13 - 13 14 14 15 15 16 16 17 - 17 18 18 19 19 20 20 21 - 21 22 22 23 23 24 24 25 - 25 26 26 27 - - 25 !NTHETA: angles - 13 14 15 7 8 9 6 7 8 - 16 17 18 15 16 17 2 3 4 - 4 5 6 9 10 11 11 12 13 - 14 15 16 1 2 3 3 4 5 - 10 11 12 12 13 14 25 26 27 - 5 6 7 8 9 10 17 18 19 - 18 19 20 22 23 24 21 22 23 - 19 20 21 20 21 22 23 24 25 - 24 25 26 - - 19 !NPHI: dihedrals - 1 2 3 4 2 3 4 5 - 3 4 5 6 4 5 6 7 - 8 9 10 11 9 10 11 12 - 10 11 12 13 11 12 13 14 - 12 13 14 15 15 16 17 18 - 16 17 18 19 17 18 19 20 - 18 19 20 21 19 20 21 22 - 20 21 22 23 21 22 23 24 - 22 23 24 25 23 24 25 26 - 24 25 26 27 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg deleted file mode 100644 index 31853cd5ad..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg deleted file mode 100644 index fdc5c890b1..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write('Data Bonds') { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write('Data Dihedrals') { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once('Data Angles By Type') { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Chaperonin { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - # i j epsilon sigma K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperonins type @atom:C - } - - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 - } - -} # Chaperonin - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 9b86809cc3..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 34c66418a8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d70ea9b1f2..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt +++ /dev/null @@ -1,45 +0,0 @@ -write_once("Data Boundary") { - 0.0 20.0 xlo xhi - 0.0 20.0 ylo yhi - 0.0 20.0 zlo zhi -} - - -import "1beadFrustrated_variants.lt" -import "chaperonin.lt" - - -protein = new 1beadMisfolded # (frustrated protein, misfolded conformation) -chaperinin = new Chaperonin # (hollow chaperonin cavity. usually immobile) - - - -# ---- Now define interactions between the atoms in the protein ---- -# ---- (named "B", "L", "N") and the atom which represents the ---- -# ---- chaperone ("C"). These interactions are tabulated. ---- - -write_once("In Settings") { - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/L table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadFrustrated/N table table_chaperonin_h=0.dat CH_H0 -} - -# Note: If you want to use a "hydrophilic" chaperone (with h=0, not h=0.475) -# then replace "table_chaperonin_h=0_475.dat CH_H0.475" -# with "table_chaperonin_h=0.dat CH_H0" - -# LAMMPS has many available force field styles (and atom styles). Here we -# select the ones which work well for the full combine system. (This should -# override any settings made in "1beadFrustrated.lt" or "chaperonin.lt") - - -write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat deleted file mode 100644 index 675d228a90..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat +++ /dev/null @@ -1,1188 +0,0 @@ -# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). -# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) - -CH_H0.475 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 -0.018422088583 0.0 -2 0.005 -0.0184221525389 2.55824082873e-05 -3 0.01 -0.0184223444081 5.11654127471e-05 -4 0.015 -0.018422664195 7.67496107175e-05 -5 0.02 -0.0184231119071 0.000102335598797 -6 0.025 -0.018423687555 0.000127923973785 -7 0.03 -0.0184243911519 0.000153515332637 -8 0.035 -0.0184252227143 0.000179110272379 -9 0.04 -0.0184261822615 0.000204709390236 -10 0.045 -0.0184272698161 0.000230313283607 -11 0.05 -0.0184284854033 0.000255922550119 -12 0.055 -0.0184298290516 0.000281537787625 -13 0.06 -0.0184313007922 0.000307159594253 -14 0.065 -0.0184329006595 0.000332788568419 -15 0.07 -0.0184346286908 0.000358425308862 -16 0.075 -0.0184364849265 0.000384070414671 -17 0.08 -0.0184384694099 0.000409724485298 -18 0.085 -0.0184405821873 0.000435388120601 -19 0.09 -0.018442823308 0.000461061920867 -20 0.095 -0.0184451928244 0.000486746486835 -21 0.1 -0.0184476907918 0.000512442419724 -22 0.105 -0.0184503172686 0.00053815032126 -23 0.11 -0.018453072316 0.000563870793707 -24 0.115 -0.0184559559985 0.00058960443989 -25 0.12 -0.0184589683834 0.000615351863219 -26 0.125 -0.0184621095411 0.000641113667723 -27 0.13 -0.018465379545 0.000666890458074 -28 0.135 -0.0184687784716 0.000692682839612 -29 0.14 -0.0184723064004 0.000718491418378 -30 0.145 -0.0184759634138 0.000744316801133 -31 0.15 -0.0184797495974 0.000770159595394 -32 0.155 -0.0184836650398 0.000796020409456 -33 0.16 -0.0184877098326 0.000821899852421 -34 0.165 -0.0184918840704 0.000847798534223 -35 0.17 -0.018496187851 0.000873717065662 -36 0.175 -0.0185006212752 0.000899656058423 -37 0.18 -0.0185051844467 0.000925616125112 -38 0.185 -0.0185098774726 0.000951597879278 -39 0.19 -0.0185147004627 0.000977601935442 -40 0.195 -0.0185196535301 0.00100362890913 -41 0.2 -0.018524736791 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5.855 626872755.056 -43125823862.6 -1173 5.86 889629660.718 -63393502739.0 -1174 5.865 1278740106.83 -94503868935.1 -1175 5.87 1863446791.23 -1.43025101229e+11 -1176 5.875 2756012237.96 -2.20012469835e+11 -1177 5.88 4141901662.1 -3.44454801129e+11 -1178 5.885 6333810219.82 -5.49690750348e+11 -1179 5.89 9870702215.02 -8.95661856872e+11 -1180 5.895 15704120493.1 -1.49296797827e+12 -1181 5.9 25558689542.6 -2.55153879404e+12 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat deleted file mode 100644 index 2ad6d7b691..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat +++ /dev/null @@ -1,1187 +0,0 @@ -# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) - -CH_H0 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 8.31299178857e-07 0.0 -2 0.005 8.31311879342e-07 -5.08022586688e-09 -3 0.01 8.31349981758e-07 -1.01608369733e-08 -4 0.015 8.31413488996e-07 -1.52422186449e-08 -5 0.02 8.31502405871e-07 -2.03247562721e-08 -6 0.025 8.31616739127e-07 -2.54088353865e-08 -7 0.03 8.31756497437e-07 -3.04948417048e-08 -8 0.035 8.319216914e-07 -3.55831611709e-08 -9 0.04 8.32112333547e-07 -4.06741800058e-08 -10 0.045 8.32328438343e-07 -4.57682847516e-08 -11 0.05 8.32570022183e-07 -5.08658623183e-08 -12 0.055 8.328371034e-07 -5.59673000292e-08 -13 0.06 8.33129702263e-07 -6.10729856679e-08 -14 0.065 8.33447840983e-07 -6.61833075238e-08 -15 0.07 8.33791543713e-07 -7.12986544391e-08 -16 0.075 8.34160836552e-07 -7.64194158551e-08 -17 0.08 8.34555747546e-07 -8.15459818584e-08 -18 0.085 8.34976306696e-07 -8.66787432278e-08 -19 0.09 8.35422545957e-07 -9.18180914814e-08 -20 0.095 8.35894499243e-07 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d660fee308..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 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0.0704439199439 -358 357.0 -2.3414076153 0.0712032738621 -359 358.0 -2.41296973939 0.0719124463259 -360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min deleted file mode 100644 index 321ba3c095..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min +++ /dev/null @@ -1,25 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -pair_write 1 4 1001 r 0.00000000001 5.05 test_chap-B.dat C-B 0 0 -pair_write 2 4 1001 r 0.00000000001 5.05 test_chap-L.dat C-L 0 0 -pair_write 3 4 1001 r 0.00000000001 5.05 test_chap-N.dat C-N 0 0 - - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt deleted file mode 100644 index 7c0855cb8d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt +++ /dev/null @@ -1,48 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.25 0.25 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50000 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 1000000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT deleted file mode 100644 index ecb9adad2e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT +++ /dev/null @@ -1,38 +0,0 @@ -# This directory demonstrates how to run a long simulation of -# the "frustrated" coarse-grained protein in the presence of one -# or more coarse-graine small ("mini") chaperones (R=3, h=0.6) as described in: -# -# AI Jewett and J-E Shea, J. Mol. Biol, Vol 363(5), (2006) -# and earlier in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# -# Because this process takes a long time (even with the help of the chaperone) -# I save the data relatively infrequently. -# -# Note: In the 2006 paper, only one protein and one chaperone was simulated. -# In this example, 8 proteins and 8 chaperones were simulated. -# -# Note: In this case, the chaperones appear to catalyze aggregation. -# This is due to an artifact in the protein model. That model -# was not designed to study aggregation. However the simulation -# is suitable for making pretty pictures (to show off moltemplate). -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index b0013ccc62..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,476 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 224 !NATOM - 1 1 2 2 0.000000 1.0000 0 - 2 1 1 1 0.000000 1.0000 0 - 3 1 2 2 0.000000 1.0000 0 - 4 1 1 1 0.000000 1.0000 0 - 5 1 2 2 0.000000 1.0000 0 - 6 1 1 1 0.000000 1.0000 0 - 7 1 3 3 0.000000 1.0000 0 - 8 1 3 3 0.000000 1.0000 0 - 9 1 1 1 0.000000 1.0000 0 - 10 1 2 2 0.000000 1.0000 0 - 11 1 1 1 0.000000 1.0000 0 - 12 1 2 2 0.000000 1.0000 0 - 13 1 1 1 0.000000 1.0000 0 - 14 1 2 2 0.000000 1.0000 0 - 15 1 3 3 0.000000 1.0000 0 - 16 1 3 3 0.000000 1.0000 0 - 17 1 3 3 0.000000 1.0000 0 - 18 1 1 1 0.000000 1.0000 0 - 19 1 1 1 0.000000 1.0000 0 - 20 1 2 2 0.000000 1.0000 0 - 21 1 2 2 0.000000 1.0000 0 - 22 1 1 1 0.000000 1.0000 0 - 23 1 1 1 0.000000 1.0000 0 - 24 1 2 2 0.000000 1.0000 0 - 25 1 2 2 0.000000 1.0000 0 - 26 1 1 1 0.000000 1.0000 0 - 27 1 2 2 0.000000 1.0000 0 - 28 2 2 2 0.000000 1.0000 0 - 29 2 1 1 0.000000 1.0000 0 - 30 2 2 2 0.000000 1.0000 0 - 31 2 1 1 0.000000 1.0000 0 - 32 2 2 2 0.000000 1.0000 0 - 33 2 1 1 0.000000 1.0000 0 - 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172 7 2 2 0.000000 1.0000 0 - 173 7 1 1 0.000000 1.0000 0 - 174 7 2 2 0.000000 1.0000 0 - 175 7 1 1 0.000000 1.0000 0 - 176 7 2 2 0.000000 1.0000 0 - 177 7 3 3 0.000000 1.0000 0 - 178 7 3 3 0.000000 1.0000 0 - 179 7 3 3 0.000000 1.0000 0 - 180 7 1 1 0.000000 1.0000 0 - 181 7 1 1 0.000000 1.0000 0 - 182 7 2 2 0.000000 1.0000 0 - 183 7 2 2 0.000000 1.0000 0 - 184 7 1 1 0.000000 1.0000 0 - 185 7 1 1 0.000000 1.0000 0 - 186 7 2 2 0.000000 1.0000 0 - 187 7 2 2 0.000000 1.0000 0 - 188 7 1 1 0.000000 1.0000 0 - 189 7 2 2 0.000000 1.0000 0 - 190 8 2 2 0.000000 1.0000 0 - 191 8 1 1 0.000000 1.0000 0 - 192 8 2 2 0.000000 1.0000 0 - 193 8 1 1 0.000000 1.0000 0 - 194 8 2 2 0.000000 1.0000 0 - 195 8 1 1 0.000000 1.0000 0 - 196 8 3 3 0.000000 1.0000 0 - 197 8 3 3 0.000000 1.0000 0 - 198 8 1 1 0.000000 1.0000 0 - 199 8 2 2 0.000000 1.0000 0 - 200 8 1 1 0.000000 1.0000 0 - 201 8 2 2 0.000000 1.0000 0 - 202 8 1 1 0.000000 1.0000 0 - 203 8 2 2 0.000000 1.0000 0 - 204 8 3 3 0.000000 1.0000 0 - 205 8 3 3 0.000000 1.0000 0 - 206 8 3 3 0.000000 1.0000 0 - 207 8 1 1 0.000000 1.0000 0 - 208 8 1 1 0.000000 1.0000 0 - 209 8 2 2 0.000000 1.0000 0 - 210 8 2 2 0.000000 1.0000 0 - 211 8 1 1 0.000000 1.0000 0 - 212 8 1 1 0.000000 1.0000 0 - 213 8 2 2 0.000000 1.0000 0 - 214 8 2 2 0.000000 1.0000 0 - 215 8 1 1 0.000000 1.0000 0 - 216 8 2 2 0.000000 1.0000 0 - 217 9 4 4 0.000000 100.0000 0 - 218 10 4 4 0.000000 100.0000 0 - 219 11 4 4 0.000000 100.0000 0 - 220 12 4 4 0.000000 100.0000 0 - 221 13 4 4 0.000000 100.0000 0 - 222 14 4 4 0.000000 100.0000 0 - 223 15 4 4 0.000000 100.0000 0 - 224 16 4 4 0.000000 100.0000 0 - - 208 !NBOND: bonds - 1 2 2 3 3 4 4 5 - 5 6 6 7 7 8 8 9 - 9 10 10 11 11 12 12 13 - 13 14 14 15 15 16 16 17 - 17 18 18 19 19 20 20 21 - 21 22 22 23 23 24 24 25 - 25 26 26 27 28 29 29 30 - 30 31 31 32 32 33 33 34 - 34 35 35 36 36 37 37 38 - 38 39 39 40 40 41 41 42 - 42 43 43 44 44 45 45 46 - 46 47 47 48 48 49 49 50 - 50 51 51 52 52 53 53 54 - 55 56 56 57 57 58 58 59 - 59 60 60 61 61 62 62 63 - 63 64 64 65 65 66 66 67 - 67 68 68 69 69 70 70 71 - 71 72 72 73 73 74 74 75 - 75 76 76 77 77 78 78 79 - 79 80 80 81 82 83 83 84 - 84 85 85 86 86 87 87 88 - 88 89 89 90 90 91 91 92 - 92 93 93 94 94 95 95 96 - 96 97 97 98 98 99 99 100 - 100 101 101 102 102 103 103 104 - 104 105 105 106 106 107 107 108 - 109 110 110 111 111 112 112 113 - 113 114 114 115 115 116 116 117 - 117 118 118 119 119 120 120 121 - 121 122 122 123 123 124 124 125 - 125 126 126 127 127 128 128 129 - 129 130 130 131 131 132 132 133 - 133 134 134 135 136 137 137 138 - 138 139 139 140 140 141 141 142 - 142 143 143 144 144 145 145 146 - 146 147 147 148 148 149 149 150 - 150 151 151 152 152 153 153 154 - 154 155 155 156 156 157 157 158 - 158 159 159 160 160 161 161 162 - 163 164 164 165 165 166 166 167 - 167 168 168 169 169 170 170 171 - 171 172 172 173 173 174 174 175 - 175 176 176 177 177 178 178 179 - 179 180 180 181 181 182 182 183 - 183 184 184 185 185 186 186 187 - 187 188 188 189 190 191 191 192 - 192 193 193 194 194 195 195 196 - 196 197 197 198 198 199 199 200 - 200 201 201 202 202 203 203 204 - 204 205 205 206 206 207 207 208 - 208 209 209 210 210 211 211 212 - 212 213 213 214 214 215 215 216 - - 200 !NTHETA: angles - 13 14 15 40 41 42 67 68 69 - 94 95 96 121 122 123 148 149 150 - 175 176 177 202 203 204 7 8 9 - 6 7 8 16 17 18 34 35 36 - 33 34 35 43 44 45 61 62 63 - 60 61 62 70 71 72 88 89 90 - 87 88 89 97 98 99 115 116 117 - 114 115 116 124 125 126 142 143 144 - 141 142 143 151 152 153 169 170 171 - 168 169 170 178 179 180 196 197 198 - 195 196 197 205 206 207 15 16 17 - 42 43 44 69 70 71 96 97 98 - 123 124 125 150 151 152 177 178 179 - 204 205 206 2 3 4 4 5 6 - 9 10 11 11 12 13 29 30 31 - 31 32 33 36 37 38 38 39 40 - 56 57 58 58 59 60 63 64 65 - 65 66 67 83 84 85 85 86 87 - 90 91 92 92 93 94 110 111 112 - 112 113 114 117 118 119 119 120 121 - 137 138 139 139 140 141 144 145 146 - 146 147 148 164 165 166 166 167 168 - 171 172 173 173 174 175 191 192 193 - 193 194 195 198 199 200 200 201 202 - 14 15 16 41 42 43 68 69 70 - 95 96 97 122 123 124 149 150 151 - 176 177 178 203 204 205 1 2 3 - 3 4 5 10 11 12 12 13 14 - 25 26 27 28 29 30 30 31 32 - 37 38 39 39 40 41 52 53 54 - 55 56 57 57 58 59 64 65 66 - 66 67 68 79 80 81 82 83 84 - 84 85 86 91 92 93 93 94 95 - 106 107 108 109 110 111 111 112 113 - 118 119 120 120 121 122 133 134 135 - 136 137 138 138 139 140 145 146 147 - 147 148 149 160 161 162 163 164 165 - 165 166 167 172 173 174 174 175 176 - 187 188 189 190 191 192 192 193 194 - 199 200 201 201 202 203 214 215 216 - 5 6 7 8 9 10 32 33 34 - 35 36 37 59 60 61 62 63 64 - 86 87 88 89 90 91 113 114 115 - 116 117 118 140 141 142 143 144 145 - 167 168 169 170 171 172 194 195 196 - 197 198 199 17 18 19 44 45 46 - 71 72 73 98 99 100 125 126 127 - 152 153 154 179 180 181 206 207 208 - 18 19 20 22 23 24 21 22 23 - 45 46 47 49 50 51 48 49 50 - 72 73 74 76 77 78 75 76 77 - 99 100 101 103 104 105 102 103 104 - 126 127 128 130 131 132 129 130 131 - 153 154 155 157 158 159 156 157 158 - 180 181 182 184 185 186 183 184 185 - 207 208 209 211 212 213 210 211 212 - 19 20 21 20 21 22 23 24 25 - 24 25 26 46 47 48 47 48 49 - 50 51 52 51 52 53 73 74 75 - 74 75 76 77 78 79 78 79 80 - 100 101 102 101 102 103 104 105 106 - 105 106 107 127 128 129 128 129 130 - 131 132 133 132 133 134 154 155 156 - 155 156 157 158 159 160 159 160 161 - 181 182 183 182 183 184 185 186 187 - 186 187 188 208 209 210 209 210 211 - 212 213 214 213 214 215 - - 152 !NPHI: dihedrals - 1 2 3 4 2 3 4 5 - 3 4 5 6 4 5 6 7 - 8 9 10 11 9 10 11 12 - 10 11 12 13 11 12 13 14 - 12 13 14 15 15 16 17 18 - 16 17 18 19 17 18 19 20 - 18 19 20 21 19 20 21 22 - 20 21 22 23 21 22 23 24 - 22 23 24 25 23 24 25 26 - 24 25 26 27 28 29 30 31 - 29 30 31 32 30 31 32 33 - 31 32 33 34 35 36 37 38 - 36 37 38 39 37 38 39 40 - 38 39 40 41 39 40 41 42 - 42 43 44 45 43 44 45 46 - 44 45 46 47 45 46 47 48 - 46 47 48 49 47 48 49 50 - 48 49 50 51 49 50 51 52 - 50 51 52 53 51 52 53 54 - 55 56 57 58 56 57 58 59 - 57 58 59 60 58 59 60 61 - 62 63 64 65 63 64 65 66 - 64 65 66 67 65 66 67 68 - 66 67 68 69 69 70 71 72 - 70 71 72 73 71 72 73 74 - 72 73 74 75 73 74 75 76 - 74 75 76 77 75 76 77 78 - 76 77 78 79 77 78 79 80 - 78 79 80 81 82 83 84 85 - 83 84 85 86 84 85 86 87 - 85 86 87 88 89 90 91 92 - 90 91 92 93 91 92 93 94 - 92 93 94 95 93 94 95 96 - 96 97 98 99 97 98 99 100 - 98 99 100 101 99 100 101 102 - 100 101 102 103 101 102 103 104 - 102 103 104 105 103 104 105 106 - 104 105 106 107 105 106 107 108 - 109 110 111 112 110 111 112 113 - 111 112 113 114 112 113 114 115 - 116 117 118 119 117 118 119 120 - 118 119 120 121 119 120 121 122 - 120 121 122 123 123 124 125 126 - 124 125 126 127 125 126 127 128 - 126 127 128 129 127 128 129 130 - 128 129 130 131 129 130 131 132 - 130 131 132 133 131 132 133 134 - 132 133 134 135 136 137 138 139 - 137 138 139 140 138 139 140 141 - 139 140 141 142 143 144 145 146 - 144 145 146 147 145 146 147 148 - 146 147 148 149 147 148 149 150 - 150 151 152 153 151 152 153 154 - 152 153 154 155 153 154 155 156 - 154 155 156 157 155 156 157 158 - 156 157 158 159 157 158 159 160 - 158 159 160 161 159 160 161 162 - 163 164 165 166 164 165 166 167 - 165 166 167 168 166 167 168 169 - 170 171 172 173 171 172 173 174 - 172 173 174 175 173 174 175 176 - 174 175 176 177 177 178 179 180 - 178 179 180 181 179 180 181 182 - 180 181 182 183 181 182 183 184 - 182 183 184 185 183 184 185 186 - 184 185 186 187 185 186 187 188 - 186 187 188 189 190 191 192 193 - 191 192 193 194 192 193 194 195 - 193 194 195 196 197 198 199 200 - 198 199 200 201 199 200 201 202 - 200 201 202 203 201 202 203 204 - 204 205 206 207 205 206 207 208 - 206 207 208 209 207 208 209 210 - 208 209 210 211 209 210 211 212 - 210 211 212 213 211 212 213 214 - 212 213 214 215 213 214 215 216 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg deleted file mode 100644 index c62a881b2a..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg deleted file mode 100644 index 38ef54396e..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write('Data Bonds') { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write('Data Dihedrals') { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once('Data Angles By Type') { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 9b86809cc3..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 34c66418a8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt deleted file mode 100644 index 1d37823b7a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Minichaperone { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - - # i j pairStyle eps sig K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 3.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperones type @atom:C - } - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 - } - -} # Minichaperone - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt deleted file mode 100644 index 8f8c37d08b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt +++ /dev/null @@ -1,72 +0,0 @@ -write_once("Data Boundary") { - 0.0 80.0 xlo xhi - 0.0 80.0 ylo yhi - 0.0 80.0 zlo zhi -} - - -import "1beadFrustrated_variants.lt" -import "minichaperone.lt" - - -# Create 8 proteins and 8 chaperones (2x2x2 array): -# NOTE: Below I create multiple proteins and multiple chaperones -# to see what would happen. (I suspect nothing good. In the -# 2006 paper, only 1 protein and 1 chaperone were present.) - - -proteins = new 1beadUnfolded [2].move(40,0,0) - [2].move(0,40,0) - [2].move(0,0,40) - -chaperones = new Minichaperone [2].move(40,0,0) - [2].move(0,40,0) - [2].move(0,0,40) - -proteins[*][*][*].move(20,20,20) # to avoid overlap with the chaperones - - - -# If you only want 1 protein and 1 chaperone -# then replace the lines above with: -# -# protein = new 1beadMisfolded -# chaperone = new Minichaperone - - - - - -# ---- Now define interactions between the atoms in the protein ---- -# ---- (named "B", "L", "N") and the atom which represents the ---- -# ---- chaperone ("c"). These interactions are tabulated. ---- - -write_once("In Settings") { - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/B table table_minichaperone_h=0.6.dat CH_H0.6 - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/L table table_minichaperone_h=0.dat CH_H0 - pair_coeff @atom:Minichaperone/C @atom:1beadFrustrated/N table table_minichaperone_h=0.dat CH_H0 -} - -# Note: If you want purely repulsive spheres (crowding, h=0.0) -# instead of an attractive "hydrophobic" chaperone (h=0.6) -# then replace "table_minichaperone_h=0_6.dat CH_H0_6" -# with "table_minichaperone_h=0.dat CH_H0" -# (... or just use an ordinary Lennard-Jones interaction -# with sigma = 6.0 and epsilon near 0.0) - - -# LAMMPS has many available force field styles (and atom styles). Here we -# select the ones which work well for the full combine system. (This should -# override any settings made in "1beadFrustrated.lt" or "minichaperone.lt") - - -write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 981 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat deleted file mode 100644 index d660fee308..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 -3.78808936748 0.080737451911 -15 14.0 -3.86866640485 0.0804036822781 -16 15.0 -3.94887077101 0.0799920342374 -17 16.0 -4.02862438516 0.0795021264757 -18 17.0 -4.10784885622 0.0789337203415 -19 18.0 -4.18646562704 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-1.85985831882 0.0672956071568 -350 349.0 -1.92773877092 0.0684595158069 -351 350.0 -1.99676540616 0.0695875914917 -352 351.0 -2.06690124527 0.0706775413231 -353 352.0 -2.13810701636 0.0717270740805 -354 353.0 -2.21034115987 0.0727339066469 -355 354.0 -2.28355983986 0.0736957705223 -356 355.0 -2.35771696194 0.0746104183955 -357 356.0 -2.43276419776 0.0754756307561 -358 357.0 -2.50865101613 0.0762892225281 -359 358.0 -2.58532472075 0.0770490497051 -360 359.0 -2.66273049463 0.0777530159679 - -# Table of the potential and its negative derivative for frustrated beta sheet -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 - -FRUSTRATED_BETA -N 360 DEGREES - -1 0.0 -2.55809068762 0.0731724739818 -2 1.0 -2.63154144494 0.0737195744566 -3 2.0 -2.70551060968 0.0742089966437 -4 3.0 -2.77993963883 0.074639023134 -5 4.0 -2.85476830901 0.0750080115297 -6 5.0 -2.92993479441 0.0753144003899 -7 6.0 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a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat deleted file mode 100644 index d2b1ed3aaf..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat +++ /dev/null @@ -1,988 +0,0 @@ -# Interaction between a chaperone wall and hydrophobic ("B") beads (h=0.6) -# Generated using: -# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True - -CH_H0.6 -N 981 R 3.1 8.0 - -1 3.1 24321971157.7 2.4400451019e+12 -2 3.105 14907528428.0 1.42456746092e+12 -3 3.11 9347010266.92 8.52735030437e+11 -4 3.115 5983057175.03 5.22187648991e+11 -5 3.12 3902942155.05 3.26496996649e+11 -6 3.125 2590648415.38 2.0808159227e+11 -7 3.13 1747350825.1 1.34970444886e+11 -8 3.135 1196139798.89 88984974583.5 -9 3.14 830130182.341 59559787515.6 -10 3.145 583518174.975 40428507749.3 -11 3.15 415078797.287 27803974550.9 -12 3.155 298562827.719 19356989964.4 -13 3.16 217001769.743 13631486848.5 -14 3.165 159270305.159 9703243449.66 -15 3.17 117976881.962 6977184032.49 -16 3.175 88149161.6455 5064988683.98 -17 3.18 66402860.1298 3710042118.5 -18 3.185 50409022.6215 2740737360.59 -19 3.19 38548170.6708 2041021063.98 -20 3.195 29683036.1074 1531572773.33 -21 3.2 23007502.8905 1157631256.92 -22 3.205 17945109.6836 881028781.898 -23 3.21 14080149.2893 674921399.554 -24 3.215 11110438.2418 520266326.167 -25 3.22 8814639.75879 403443800.764 -26 3.225 7029455.47123 314636408.027 -27 3.23 5633571.16439 246714657.082 -28 3.235 4536265.59262 194464091.949 -29 3.24 3669265.83647 154044868.616 -30 3.245 2980881.1453 122610915.077 -31 3.25 2431748.15466 98039536.8272 -32 3.255 1991724.07297 78738058.3506 -33 3.26 1637603.46485 63504600.2322 -34 3.265 1351429.90872 51427172.534 -35 3.27 1119240.11293 41810074.9071 -36 3.275 930124.378436 34119886.2947 -37 3.28 775519.857832 27945597.578 -38 3.285 648676.115123 22969017.4933 -39 3.29 544248.919174 18942684.9889 -40 3.295 457989.984944 15673297.5619 -41 3.3 386508.875651 13009215.1485 -42 3.305 327089.446276 10830991.226 -43 3.31 277547.709074 9044163.93118 -44 3.315 236121.303553 7573742.76366 -45 3.32 201383.18845 6359973.47163 -46 3.325 172173.978278 5355070.91875 -47 3.33 147548.691578 4520688.28477 -48 3.335 126734.684289 3825948.80978 -49 3.34 109098.298235 3245909.11014 -50 3.345 94118.3261235 2760354.93052 -51 3.35 81364.827777 2352853.97713 -52 3.355 70482.1624146 2010008.31682 -53 3.36 61175.3541703 1720862.26897 -54 3.365 53199.1018261 1476431.88582 -55 3.37 46348.8930587 1269329.84244 -56 3.375 40453.7990113 1093465.44786 -57 3.38 35370.6146686 943803.998782 -58 3.385 30979.0803706 816173.162054 -59 3.39 27177.9744013 707106.743488 -60 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-87 3.53 1180.71448694 23071.7118275 -88 3.535 1071.23498579 20764.0187577 -89 3.54 972.661050857 18704.4087568 -90 3.545 883.825202407 16864.3326446 -91 3.55 803.693750954 15218.7418698 -92 3.555 731.350460573 13745.6331832 -93 3.56 665.982328363 12425.6558809 -94 3.565 606.867190408 11241.7725673 -95 3.57 553.362906393 10178.9657593 -96 3.575 504.897910387 9223.98381086 -97 3.58 460.962945446 8365.12060921 -98 3.585 421.103825306 7592.02431669 -99 3.59 384.915088285 6895.53112553 -100 3.595 352.034427161 6267.5205811 -101 3.6 322.137794751 5700.78952663 -102 3.605 294.935098544 5188.94214534 -103 3.61 270.166409464 4726.29393494 -104 3.615 247.598619855 4307.78775517 -105 3.62 227.022494431 3928.92034957 -106 3.625 208.250065337 3585.67796495 -107 3.63 191.112328875 3274.47988201 -108 3.635 175.457206974 2992.12883298 -109 3.64 161.147741205 2735.76742147 -110 3.645 148.060491326 2502.83977901 -111 3.65 136.084113848 2291.05779528 -112 3.655 125.118099223 2098.37134728 -113 3.66 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-3.09346599767e-05 -0.00207982254527 -979 7.99 -2.05648617073e-05 -0.00206810960966 -980 7.995 -1.0253435891e-05 -0.00205647346771 -981 8.0 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat deleted file mode 100644 index 82eaa7e158..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat +++ /dev/null @@ -1,989 +0,0 @@ -# Interaction between a chaperone wall and hydrophilic ("L", "N") beads (h=0.0) -# Generated using: -# generate_tables/calc_chaperone_table.py 1.0 1.0 3.0 0.00 3.1 8.0 981 True - -CH_H0 -N 981 R 3.1 8.0 - -1 3.1 24322007640.7 2.44004657299e+12 -2 3.105 14907558394.3 1.42456861215e+12 -3 3.11 9347035105.18 8.52735941633e+11 -4 3.115 5983077933.86 5.22188377701e+11 -5 3.12 3902959636.31 3.26497584961e+11 -6 3.125 2590663239.27 2.08082071378e+11 -7 3.13 1747363476.38 1.34970838198e+11 -8 3.135 1196150660.14 88985299862.7 -9 3.14 830139558.184 59560058382.9 -10 3.145 583526310.01 40428734750.9 -11 3.15 415085889.414 27804165925.8 -12 3.155 298569038.21 19357152203.7 -13 3.16 217007230.904 13631625105.8 -14 3.165 159275126.218 9703361847.17 -15 3.17 117981153.625 6977285889.84 -16 3.175 88152959.6539 5065076691.93 -17 3.18 66406248.0614 3710118471.36 -18 3.185 50412054.1061 2740803858.1 -19 3.19 38550891.1571 2041079190.29 -20 3.195 29685484.2812 1531623758.63 -21 3.2 23009711.8183 1157676125.86 -22 3.205 17947107.7408 881068391.885 -23 3.21 14081960.9175 674956471.214 -24 3.215 11112084.5698 520297467.685 -25 3.22 8816139.11379 403471527.483 -26 3.225 7030823.80219 314661158.279 -27 3.23 5634822.39381 246736805.049 -28 3.235 4537411.91017 194483958.161 -29 3.24 3670317.94503 154062728.557 -30 3.245 2981848.4679 122627006.268 -31 3.25 2432639.00923 98054064.6797 -32 3.255 1992545.82032 78751201.0309 -33 3.26 1638362.63452 63516512.707 -34 3.265 1352132.30623 51437989.9558 -35 3.27 1119890.91156 41819915.4536 -36 3.275 930728.197936 34128853.5593 -37 3.28 776080.832192 27953782.5881 -38 3.285 649197.950984 22976500.4202 -39 3.29 544734.946388 18949536.6006 -40 3.295 458443.200409 15679580.461 -41 3.3 386931.981432 13014984.83 -42 3.305 327484.882814 10836296.983 -43 3.31 277917.684205 9049049.63384 -44 3.315 236467.817902 7578247.52911 -45 3.32 201708.057716 6364132.2427 -46 3.325 172478.852825 5358914.96458 -47 3.33 147835.073691 4524245.63494 -48 3.335 127003.943407 3829244.63171 -49 3.34 109351.684422 3248966.03768 -50 3.345 94356.982001 2763193.35086 -51 3.35 81589.7991199 2355492.28163 -52 3.355 70694.4075656 2012463.12085 -53 3.36 61375.7524283 1723148.60489 -54 3.365 53388.4609277 1478563.37272 -55 3.37 46527.9558627 1271318.83571 -56 3.375 40623.2494805 1095323.17118 -57 3.38 35531.0832305 945540.660872 -58 3.385 31131.1487289 817798.059995 -59 3.39 27322.1798598 708628.354433 -60 3.395 24018.7487675 615144.330958 -61 3.4 21148.6321858 534935.990585 -62 3.405 18650.6411473 465987.08561 -63 3.41 16472.8281676 406607.038172 -64 3.415 14571.00272 355375.264352 -65 3.42 12907.4991276 311095.530355 -66 3.425 11450.1516342 272758.442538 -67 3.43 10171.439929 239510.549012 -68 3.435 9047.7752383 210628.82877 -69 3.44 8058.90260095 185499.581541 -70 3.445 7187.39938846 163600.920836 -71 3.45 6418.25372556 144488.223969 -72 3.455 5738.50938334 127782.014261 -73 3.46 5136.9660889 113157.848128 -74 3.465 4603.92612777 100337.85845 -75 3.47 4130.97969454 89083.6690543 -76 3.475 3710.8227393 79190.4466465 -77 3.48 3337.10211855 70481.8981958 -78 3.485 3004.28373073 62806.0557792 -79 3.49 2707.54003568 56031.718535 -80 3.495 2442.65394998 50045.4440029 -81 3.5 2205.93660145 44748.9996316 -82 3.505 1994.15683268 40057.2004294 -83 3.51 1804.48068152 35896.0712099 -84 3.515 1634.41934741 32201.2821773 -85 3.52 1481.78438725 28916.8150767 -86 3.525 1344.64907977 25993.8241582 -87 3.53 1221.31506159 23389.6620133 -88 3.535 1110.28347503 21067.0451721 -89 3.54 1010.22998333 18993.3383579 -90 3.545 919.9831055 17139.9396418 -91 3.55 838.505404885 15481.7515237 -92 3.555 764.877134293 13996.7253013 -93 3.56 698.281998657 12665.4680354 -94 3.565 637.994745566 11470.9030593 -95 3.57 583.370335637 10397.9763514 -96 3.575 533.834480178 9433.40224818 -97 3.58 488.875363677 8565.44294671 -98 3.585 448.036394307 7783.71706925 -99 3.59 410.909847488 7079.03325566 -100 3.595 377.131286207 6443.24533767 -101 3.6 346.374657747 5869.126147 -102 3.605 318.34798013 5350.25743201 -103 3.61 292.789543287 4880.93371692 -104 3.615 269.464560006 4456.07824337 -105 3.62 248.162210353 4071.16939457 -106 3.625 228.693030668 3722.17622503 -107 3.63 210.886604667 3405.5019084 -108 3.635 194.589519671 3117.93407879 -109 3.64 179.663555764 2856.60118023 -110 3.645 165.984079802 2618.93405823 -111 3.65 153.438619766 2402.63212994 -112 3.655 141.925598023 2205.6335579 -113 3.66 131.353204775 2026.08892777 -114 3.665 121.638395266 1862.33799643 -115 3.67 112.705996374 1712.88913275 -116 3.675 104.487909965 1576.40112248 -117 3.68 96.9224019089 1451.66705065 -118 3.685 89.9534670245 1337.6000114 -119 3.69 83.5302613658 1233.22042683 -120 3.695 77.6065942935 1137.6447839 -121 3.7 72.1404736708 1050.07562216 -122 3.705 67.0936983024 969.792625804 -123 3.71 62.431492423 896.144691745 -124 3.715 58.1221776441 828.54286083 -125 3.72 54.1368782948 766.454013201 -126 3.725 50.4492565603 709.395240693 -127 3.73 47.0352742263 656.928819585 -128 3.735 43.8729782026 608.65771617 -129 3.74 40.9423073113 564.221565572 -130 3.745 38.2249181088 523.293071279 -131 3.75 35.7040277571 485.57477893 -132 3.755 33.3642721761 450.796183363 -133 3.76 31.1915779041 418.711132572 -134 3.765 29.1730462649 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67.0913657925 -161 3.9 5.54461511838 63.0285320059 -162 3.905 5.23907089671 59.2319187891 -163 3.91 4.95188356739 55.6827704829 -164 3.915 4.68185972707 52.3637443466 -165 3.92 4.42788939186 49.2587972858 -166 3.925 4.18893976204 46.353082203 -167 3.93 3.96404948281 43.6328531095 -168 3.935 3.75232335915 41.0853782151 -169 3.94 3.55292748687 38.6988602882 -170 3.945 3.36508476491 36.4623636443 -171 3.95 3.18807075749 34.3657471793 -172 3.955 3.021209877 32.3996029206 -173 3.96 2.86387186138 30.5551996145 -174 3.965 2.71546852189 28.8244309147 -175 3.97 2.57545073925 27.1997677761 -176 3.975 2.44330568809 25.6742146917 -177 3.98 2.31855427126 24.2412694474 -178 3.985 2.20074874724 22.8948860937 -179 3.99 2.08947053515 21.6294408646 -180 3.995 1.98432818342 20.4397007945 -181 4.0 1.88495548901 19.3207948084 -182 4.005 1.79100975549 18.2681870794 -183 4.01 1.70217017901 17.2776524655 -184 4.015 1.61813635232 16.3452538542 -185 4.02 1.53862687753 15.467321259 -186 4.025 1.4633780794 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7.795 5.402401468e-08 3.33222289779e-07 -941 7.8 5.23679304898e-08 3.29220126433e-07 -942 7.805 5.07317266285e-08 3.25270035737e-07 -943 7.81 4.91151445613e-08 3.21371288087e-07 -944 7.815 4.75179293742e-08 3.17523164833e-07 -945 7.82 4.59398297194e-08 3.13724958102e-07 -946 7.825 4.43805977617e-08 3.09975970624e-07 -947 7.83 4.28399891263e-08 3.06275515564e-07 -948 7.835 4.13177628469e-08 3.02622916355e-07 -949 7.84 3.98136813144e-08 2.99017506534e-07 -950 7.845 3.83275102273e-08 2.95458629582e-07 -951 7.85 3.68590185422e-08 2.91945638765e-07 -952 7.855 3.54079784251e-08 2.8847789698e-07 -953 7.86 3.39741652039e-08 2.85054776599e-07 -954 7.865 3.25573573211e-08 2.81675659322e-07 -955 7.87 3.11573362879e-08 2.78339936025e-07 -956 7.875 2.97738866382e-08 2.7504700662e-07 -957 7.88 2.84067958844e-08 2.71796279909e-07 -958 7.885 2.70558544725e-08 2.68587173443e-07 -959 7.89 2.57208557397e-08 2.65419113385e-07 -960 7.895 2.44015958707e-08 2.62291534374e-07 -961 7.9 2.30978738564e-08 2.59203879393e-07 -962 7.905 2.18094914519e-08 2.56155599635e-07 -963 7.91 2.05362531363e-08 2.53146154374e-07 -964 7.915 1.92779660724e-08 2.50175010842e-07 -965 7.92 1.8034440067e-08 2.47241644098e-07 -966 7.925 1.68054875325e-08 2.44345536912e-07 -967 7.93 1.55909234484e-08 2.41486179638e-07 -968 7.935 1.43905653237e-08 2.38663070101e-07 -969 7.94 1.32042331597e-08 2.35875713474e-07 -970 7.945 1.20317494138e-08 2.33123622171e-07 -971 7.95 1.08729389636e-08 2.30406315726e-07 -972 7.955 9.72762907123e-09 2.27723320689e-07 -973 7.96 8.59564934896e-09 2.2507417051e-07 -974 7.965 7.47683172465e-09 2.2245840544e-07 -975 7.97 6.37101040818e-09 2.19875572416e-07 -976 7.975 5.27802185823e-09 2.17325224966e-07 -977 7.98 4.19770474957e-09 2.148069231e-07 -978 7.985 3.12989994095e-09 2.12320233213e-07 -979 7.99 2.07445044336e-09 2.09864727985e-07 -980 7.995 1.03120138888e-09 2.07439986287e-07 -981 8.0 0.0 0.0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min deleted file mode 100644 index e2d4a5cce4..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min +++ /dev/null @@ -1,24 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# Optional: Make sure the pairwise energies look reasonable: -pair_write 1 4 1001 r 4.05 8 test_chap-B.dat C-B 0 0 -pair_write 2 4 1001 r 4.05 8 test_chap-L.dat C-L 0 0 -pair_write 3 4 1001 r 4.05 8 test_chap-N.dat C-N 0 0 - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt deleted file mode 100644 index 523a16575a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.25 0.25 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 5000 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 1000000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT deleted file mode 100644 index 77af3de15a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README.TXT +++ /dev/null @@ -1,29 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# During this short simulation (run_short_sim.nvt.in) the protein evolves -# from an unfolded initial conformation to a misfolded conformation. -# (Visualize using VMD. Note: It can take hundreds of millions of -# timesteps to escape from this conformation and reach the folded state.) -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh deleted file mode 100755 index 99338c7708..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_run.sh +++ /dev/null @@ -1,21 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - -# ----------------------------------- - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run_short_sim.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index c7f8572b29..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,85 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 27 !NATOM - 1 1 2 2 0.000000 1.0000 0 - 2 1 1 1 0.000000 1.0000 0 - 3 1 2 2 0.000000 1.0000 0 - 4 1 1 1 0.000000 1.0000 0 - 5 1 2 2 0.000000 1.0000 0 - 6 1 1 1 0.000000 1.0000 0 - 7 1 3 3 0.000000 1.0000 0 - 8 1 3 3 0.000000 1.0000 0 - 9 1 1 1 0.000000 1.0000 0 - 10 1 2 2 0.000000 1.0000 0 - 11 1 1 1 0.000000 1.0000 0 - 12 1 2 2 0.000000 1.0000 0 - 13 1 1 1 0.000000 1.0000 0 - 14 1 2 2 0.000000 1.0000 0 - 15 1 3 3 0.000000 1.0000 0 - 16 1 3 3 0.000000 1.0000 0 - 17 1 3 3 0.000000 1.0000 0 - 18 1 1 1 0.000000 1.0000 0 - 19 1 1 1 0.000000 1.0000 0 - 20 1 2 2 0.000000 1.0000 0 - 21 1 2 2 0.000000 1.0000 0 - 22 1 1 1 0.000000 1.0000 0 - 23 1 1 1 0.000000 1.0000 0 - 24 1 2 2 0.000000 1.0000 0 - 25 1 2 2 0.000000 1.0000 0 - 26 1 1 1 0.000000 1.0000 0 - 27 1 2 2 0.000000 1.0000 0 - - 26 !NBOND: bonds - 1 2 2 3 3 4 4 5 - 5 6 6 7 7 8 8 9 - 9 10 10 11 11 12 12 13 - 13 14 14 15 15 16 16 17 - 17 18 18 19 19 20 20 21 - 21 22 22 23 23 24 24 25 - 25 26 26 27 - - 25 !NTHETA: angles - 13 14 15 7 8 9 6 7 8 - 16 17 18 15 16 17 2 3 4 - 4 5 6 9 10 11 11 12 13 - 14 15 16 1 2 3 3 4 5 - 10 11 12 12 13 14 25 26 27 - 5 6 7 8 9 10 17 18 19 - 18 19 20 22 23 24 21 22 23 - 19 20 21 20 21 22 23 24 25 - 24 25 26 - - 19 !NPHI: dihedrals - 1 2 3 4 2 3 4 5 - 3 4 5 6 4 5 6 7 - 8 9 10 11 9 10 11 12 - 10 11 12 13 11 12 13 14 - 12 13 14 15 15 16 17 18 - 16 17 18 19 17 18 19 20 - 18 19 20 21 19 20 21 22 - 20 21 22 23 21 22 23 24 - 22 23 24 25 23 24 25 26 - 24 25 26 27 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg deleted file mode 100644 index 0869126bd0..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg deleted file mode 100644 index 357bc780a2..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index 074b55c735..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt +++ /dev/null @@ -1,216 +0,0 @@ -# This file defines the "frustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadFrustrated { - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.92636654 -1.8409904 -2.1482679 - $atom:a2 $mol @atom:B 0.0 -0.57313354 -1.0670787 -1.6182341 - $atom:a3 $mol @atom:L 0.0 -0.85707399 -1.2358703 -0.69350966 - $atom:a4 $mol @atom:B 0.0 -0.44231274 -0.4584993 -0.23418709 - $atom:a5 $mol @atom:L 0.0 -0.75081182 -0.62868078 0.69786737 - $atom:a6 $mol @atom:B 0.0 -0.36201977 0.11619615 1.2249098 - $atom:a7 $mol @atom:N 0.0 -0.63708237 -0.15973084 2.1723919 - $atom:a8 $mol @atom:N 0.0 0.20516047 0.10417157 2.624901 - $atom:a9 $mol @atom:B 0.0 0.57223743 0.44728103 1.7695617 - $atom:a10 $mol @atom:L 0.0 0.77646279 -0.40630393 1.3168043 - $atom:a11 $mol @atom:B 0.0 0.45475664 -0.2077937 0.40045721 - $atom:a12 $mol @atom:L 0.0 0.72712495 -1.0397637 -0.087614951 - $atom:a13 $mol @atom:B 0.0 0.36971183 -0.85840501 -0.9933019 - $atom:a14 $mol @atom:L 0.0 0.74784336 -1.5700415 -1.5859217 - $atom:a15 $mol @atom:N 0.0 0.43423905 -1.2758917 -2.4853429 - $atom:a16 $mol @atom:N 0.0 0.70583191 -0.30726921 -2.4987711 - $atom:a17 $mol @atom:N 0.0 -0.091688915 0.23323014 -2.2051358 - $atom:a18 $mol @atom:B 0.0 -0.34243283 -0.035822049 -1.2644719 - $atom:a19 $mol @atom:B 0.0 0.41961247 0.18475451 -0.65971014 - $atom:a20 $mol @atom:L 0.0 0.51968465 1.1546791 -0.77877053 - $atom:a21 $mol @atom:L 0.0 -0.40827985 1.2765273 -0.52550748 - $atom:a22 $mol @atom:B 0.0 -0.368141 0.58090904 0.19152224 - $atom:a23 $mol @atom:B 0.0 0.40327249 0.86101769 0.7336255 - $atom:a24 $mol @atom:L 0.0 0.22707289 1.8326235 0.89673346 - $atom:a25 $mol @atom:L 0.0 -0.66500182 1.7285809 1.2783166 - $atom:a26 $mol @atom:B 0.0 -0.39205603 1.0475436 1.9328097 - $atom:a27 $mol @atom:L 0.0 0.25339027 1.5246265 2.5388463 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - - $dihedral:d1 @dihedral:beta $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2 @dihedral:beta $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3 @dihedral:beta $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4 @dihedral:beta $atom:a4 $atom:a5 $atom:a6 $atom:a7 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d5 \@dihedral:turn $atom:a5 $atom:a6 $atom:a7 $atom:a8 - # \$dihedral:d6 \@dihedral:turn $atom:a6 $atom:a7 $atom:a8 $atom:a9 - # \$dihedral:d7 \@dihedral:turn $atom:a7 $atom:a8 $atom:a9 $atom:a10 - - $dihedral:d8 @dihedral:beta $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9 @dihedral:beta $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10 @dihedral:beta $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11 @dihedral:beta $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12 @dihedral:beta $atom:a12 $atom:a13 $atom:a14 $atom:a15 - - # Dihedral angle forces in the turn regions were switched off - # (in this model) so just I comment them out (and \ the variable names). - # \$dihedral:d13 \@dihedral:turn $atom:a13 $atom:a14 $atom:a15 $atom:a16 - # \$dihedral:d14 \@dihedral:turn $atom:a14 $atom:a15 $atom:a16 $atom:a17 - - $dihedral:d15 @dihedral:alpha $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16 @dihedral:alpha $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17 @dihedral:alpha $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18 @dihedral:alpha $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19 @dihedral:alpha $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20 @dihedral:alpha $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21 @dihedral:alpha $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22 @dihedral:alpha $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23 @dihedral:alpha $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24 @dihedral:alpha $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadFrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - - # We use tabular dihedral potentials to implement the dihedral forces. - # (Actually there is a way to use Fourier series, using multiple charmm - # style dihedral interactions, but it's slower and messier.) - - write_once("In Settings") { - # style file keyword - dihedral_coeff @dihedral:alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @dihedral:beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadFrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid table spline 360 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadFrustrated - - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt +++ /dev/null @@ -1,85 +0,0 @@ -import "1beadFrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadMisfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated". - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -0.69801399 -0.22114168 -1.9464876 - $atom:a2 $mol @atom:B 0.0 -0.40921658 -0.027063664 -1.0033251 - $atom:a3 $mol @atom:L 0.0 0.10259348 0.80836418 -1.0737085 - $atom:a4 $mol @atom:B 0.0 0.25857916 1.0054984 -0.11621451 - $atom:a5 $mol @atom:L 0.0 0.8258629 1.8325549 -0.18529135 - $atom:a6 $mol @atom:B 0.0 0.91366257 2.1950317 0.74175977 - $atom:a7 $mol @atom:N 0.0 1.4399539 1.554238 1.2994409 - $atom:a8 $mol @atom:N 0.0 0.73372573 1.0161012 1.7397275 - $atom:a9 $mol @atom:B 0.0 0.26608782 0.65302497 0.94353938 - $atom:a10 $mol @atom:L 0.0 0.97442305 0.13574211 0.50586398 - $atom:a11 $mol @atom:B 0.0 0.35889617 -0.18247555 -0.1764186 - $atom:a12 $mol @atom:L 0.0 0.87151735 -0.77260824 -0.75240916 - $atom:a13 $mol @atom:B 0.0 0.047726486 -1.0530682 -1.1902704 - $atom:a14 $mol @atom:L 0.0 0.34530697 -1.7476773 -1.8393331 - $atom:a15 $mol @atom:N 0.0 0.65865186 -2.45948 -1.2167056 - $atom:a16 $mol @atom:N 0.0 -0.16534524 -2.6219442 -0.67112167 - $atom:a17 $mol @atom:N 0.0 -0.010590421 -2.2445242 0.24748633 - $atom:a18 $mol @atom:B 0.0 0.18135771 -1.2564919 0.1767523 - $atom:a19 $mol @atom:B 0.0 -0.57472665 -0.82852797 -0.27027791 - $atom:a20 $mol @atom:L 0.0 -1.3967448 -1.0516787 0.24247346 - $atom:a21 $mol @atom:L 0.0 -1.003428 -0.85642681 1.1107555 - $atom:a22 $mol @atom:B 0.0 -0.25156735 -0.3182346 0.74262946 - $atom:a23 $mol @atom:B 0.0 -0.61751956 0.30115562 0.070426493 - $atom:a24 $mol @atom:L 0.0 -1.3347934 0.83310182 0.52625934 - $atom:a25 $mol @atom:L 0.0 -0.83315257 1.270904 1.2564086 - $atom:a26 $mol @atom:B 0.0 -0.10469759 1.6988523 0.72597181 - $atom:a27 $mol @atom:L 0.0 -0.57854905 2.3367737 0.11206868 - } - -} # 1beadMisfolded - - -1beadUnfolded inherits 1beadFrustrated { - - # This molecule "inherits" all of its features from "1beadFrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py deleted file mode 100755 index 34c66418a8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py +++ /dev/null @@ -1,67 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of dihedral angle interactions used in the alpha-helix -# and beta-sheet regions of the frustrated protein model described in -# provided in figure 8 of the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# Note that the "A" and "B" parameters were incorrectly reported to be -# 5.4*epsilon and 6.0*epsilon. The values used were 5.6 and 6.0 epsilon. -# The phiA and phiB values were 57.29577951308232 degrees (1 rad) -# and 180 degrees, respectively. Both expA and expB were 6.0. -# -# To generate the table used for the alpha-helix (1 degree resolution) use this: -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 -# To generate the table used for the beta-sheets (1 degree resolution) use this: -# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360 -# -# (If you're curious as to why I set the location of the minima at phi_alpha -# to 1.0 radians (57.2957795 degrees), there was no particularly good reason. -# I think the correct value turns out to be something closer to 50 degrees.) - - -from math import * -import sys - - -# The previous version included the repulsive core term -def U(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = pow(cos(0.5*(phi-phiA)*conv_units), expA) - termB = pow(cos(0.5*(phi-phiB)*conv_units), expB) - return -A*termA - B*termB - -# The previous version included the repulsive core term -def F(phi, A, phiA, expA, B, phiB, expB, use_radians=False): - conv_units = pi/180.0 - if use_radians: - conv_units = 1.0 - termA = (0.5*sin(0.5*(phi-phiA)*conv_units) * - expA * pow(cos(0.5*(phi-phiA)*conv_units), expA-1.0)) - termB = (0.5*sin(0.5*(phi-phiB)*conv_units) * - expB * pow(cos(0.5*(phi-phiB)*conv_units), expB-1.0)) - return -conv_units*(A*termA + B*termB) - -if len(sys.argv) != 10: - sys.stderr.write("Error: expected 9 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" A phiA expA B phiB expB phiMin phiMax N\n\n") - sys.exit(-1) - -A = float(sys.argv[1]) -phiA = float(sys.argv[2]) -expA = float(sys.argv[3]) -B = float(sys.argv[4]) -phiB = float(sys.argv[5]) -expB = float(sys.argv[6]) -phi_min = float(sys.argv[7]) -phi_max = float(sys.argv[8]) -N = int(sys.argv[9]) - -for i in range(0,N): - phi = phi_min + i*(phi_max - phi_min)/(N-1) - U_phi = U(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - F_phi = F(phi, A, phiA, expA, B, phiB, expB, use_radians=False) - print(str(i+1)+' '+str(phi)+' '+str(U_phi)+' '+str(F_phi)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt deleted file mode 100644 index a27595559e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "1beadFrustrated_variants.lt" - - -protein = new 1beadUnfolded - - - -# Note: The protein begins in an "Unfolded" conformation. If instead -# you want it to begin in the folded or misfolded conformations use: -# protein = new 1beadFrustrated # or -# protein = new 1beadMisfolded - - - -# ("27.0" is the length of the protein when maximally extended) -write_once("Data Boundary") { - 0.0 27.0 xlo xhi - 0.0 27.0 ylo yhi - 0.0 27.0 zlo zhi -} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat deleted file mode 100644 index d660fee308..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat +++ /dev/null @@ -1,735 +0,0 @@ -# Table of the potential and its negative derivative for frustrated alpha helix -# (Note: Derivatives are in units of energy/radians, not energy/degrees.) -# ./calc_dihedral_table.py 6.0 57.29577951308232 6 5.6 180 6 0.0 359 360 - -FRUSTRATED_ALPHA -N 360 DEGREES - -1 0.0 -2.74081145103 0.0783990792662 -2 1.0 -2.81950869101 0.0789852583442 -3 2.0 -2.89876136749 0.0795096391909 -4 3.0 -2.97850675562 0.0799703813963 -5 4.0 -3.05868032959 0.0803657243943 -6 5.0 -3.13921584545 0.0806939935737 -7 6.0 -3.22004543014 0.0809536062381 -8 7.0 -3.30109967628 0.0811430773977 -9 8.0 -3.38230774267 0.0812610253741 -10 9.0 -3.46359746038 0.0813061772009 -11 10.0 -3.54489544401 0.0812773738039 -12 11.0 -3.62612720812 0.0811735749433 -13 12.0 -3.70721728841 0.0809938639029 -14 13.0 -3.78808936748 0.080737451911 -15 14.0 -3.86866640485 0.0804036822781 -16 15.0 -3.94887077101 0.0799920342374 -17 16.0 -4.02862438516 0.0795021264757 -18 17.0 -4.10784885622 0.0789337203415 -19 18.0 -4.18646562704 0.0782867227197 -20 19.0 -4.26439612115 0.0775611885609 -21 20.0 -4.34156189202 0.0767573230567 -22 21.0 -4.41788477419 0.0758754834523 -23 22.0 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt deleted file mode 100644 index 2974c12e8a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt +++ /dev/null @@ -1,50 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.25 0.25 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.25 -# which is the folding temperature for the frustrated protein -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -# Just run it long enough for it to collapse (not fold) -# (If you need to run it longer, then dump trajectory data less frequently.) -run 50000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT deleted file mode 100644 index 5da41b9a8b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT +++ /dev/null @@ -1,32 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "unfrustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# In this example, the protein is placed inside a repulsive sphere -# of radius 6.0 sigma which confines its motion. -# (This sphere is sometimes called the "chaperonin", because -# we were using it to model the crude behavior of a chaperonin cavity.) -# -# During this short simulation (run.in.nvt) the protein evolves -# from an unfolded initial conformation to the folded state. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh +++ /dev/null @@ -1,24 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - cp -r table*.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 7763505c0d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,98 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 28 !NATOM - 1 1 1 1 0.000000 100.0000 0 - 2 2 3 3 0.000000 1.0000 0 - 3 2 2 2 0.000000 1.0000 0 - 4 2 3 3 0.000000 1.0000 0 - 5 2 2 2 0.000000 1.0000 0 - 6 2 3 3 0.000000 1.0000 0 - 7 2 2 2 0.000000 1.0000 0 - 8 2 4 4 0.000000 1.0000 0 - 9 2 4 4 0.000000 1.0000 0 - 10 2 2 2 0.000000 1.0000 0 - 11 2 3 3 0.000000 1.0000 0 - 12 2 2 2 0.000000 1.0000 0 - 13 2 3 3 0.000000 1.0000 0 - 14 2 2 2 0.000000 1.0000 0 - 15 2 3 3 0.000000 1.0000 0 - 16 2 4 4 0.000000 1.0000 0 - 17 2 4 4 0.000000 1.0000 0 - 18 2 4 4 0.000000 1.0000 0 - 19 2 2 2 0.000000 1.0000 0 - 20 2 2 2 0.000000 1.0000 0 - 21 2 3 3 0.000000 1.0000 0 - 22 2 3 3 0.000000 1.0000 0 - 23 2 2 2 0.000000 1.0000 0 - 24 2 2 2 0.000000 1.0000 0 - 25 2 3 3 0.000000 1.0000 0 - 26 2 3 3 0.000000 1.0000 0 - 27 2 2 2 0.000000 1.0000 0 - 28 2 3 3 0.000000 1.0000 0 - - 26 !NBOND: bonds - 2 3 3 4 4 5 5 6 - 6 7 7 8 8 9 9 10 - 10 11 11 12 12 13 13 14 - 14 15 15 16 16 17 17 18 - 18 19 19 20 20 21 21 22 - 22 23 23 24 24 25 25 26 - 26 27 27 28 - - 25 !NTHETA: angles - 3 4 5 5 6 7 10 11 12 - 12 13 14 8 9 10 7 8 9 - 17 18 19 19 20 21 23 24 25 - 22 23 24 2 3 4 4 5 6 - 11 12 13 13 14 15 26 27 28 - 15 16 17 6 7 8 9 10 11 - 14 15 16 18 19 20 20 21 22 - 21 22 23 24 25 26 25 26 27 - 16 17 18 - - 43 !NPHI: dihedrals - 2 3 4 5 2 3 4 5 - 3 4 5 6 3 4 5 6 - 4 5 6 7 4 5 6 7 - 5 6 7 8 5 6 7 8 - 6 7 8 9 7 8 9 10 - 8 9 10 11 9 10 11 12 - 9 10 11 12 10 11 12 13 - 10 11 12 13 11 12 13 14 - 11 12 13 14 12 13 14 15 - 12 13 14 15 13 14 15 16 - 13 14 15 16 14 15 16 17 - 15 16 17 18 16 17 18 19 - 16 17 18 19 17 18 19 20 - 17 18 19 20 18 19 20 21 - 18 19 20 21 19 20 21 22 - 19 20 21 22 20 21 22 23 - 20 21 22 23 21 22 23 24 - 21 22 23 24 22 23 24 25 - 22 23 24 25 23 24 25 26 - 23 24 25 26 24 25 26 27 - 24 25 26 27 25 26 27 28 - 25 26 27 28 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg deleted file mode 100644 index a0da344db5..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg deleted file mode 100644 index a1aa5bd855..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt +++ /dev/null @@ -1,255 +0,0 @@ -# This file defines a pair of coarse-grained protein models used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadUnfrustrated { - - # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 - $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 - $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 - $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 - $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 - $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 - $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 - $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 - $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 - $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 - $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 - $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 - $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 - $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 - $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 - $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 - $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 - $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 - $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 - $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 - $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 - $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 - $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 - $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 - $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 - $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 - $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - # - # Note that some quartets of atoms are listed because their - # potentials contain multiple terms in the Fourier expansion. - # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) - # - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 - $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 - $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 - $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 - $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 - $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadUnfrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d - # parameters. I'm hoping this will be fixed eventually. - - write_once("In Settings") { - # Correct version: - #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 - # Correct version: - #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 - dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 - dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 - dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 - # Correct version: - # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 - # Replacing with - dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 - dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 - dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 - dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadUnfrustrated - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "1beadUnfrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadUnfolded inherits 1beadUnfrustrated { - - # This molecule "inherits" all of its features from "1beadUnfrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt +++ /dev/null @@ -1,41 +0,0 @@ -# Here we define a trivial molecule containing only one particle. - -Chaperonin { - - # atomID molID atomType charge x y z - - write("Data Atoms") { - $atom:C $mol @atom:C 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:C 100.0 - } - - write_once("In Settings") { - # If for some reason there are multiple chaperones present, - # I assume that they interact repulsively (hence, L=0) - # i j epsilon sigma K L - - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm/inter 1.0 6.0 1 0 - - # Optional: define the atoms in the "chaperonins" group: - # (Defining a group for the chaperone makes it easy to immobilize it later.) - - group chaperonins type @atom:C - } - - - # Specify which pair_styles, and atom styles work well with - # this model. (Again this can be overridden later.) - - write_once("In Init") { - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 11.0 12.0 - } - -} # Chaperonin - -# We have not specified how this particle interacts with other particles -# besides itself. Later on you must do this. diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py deleted file mode 100755 index 9b86809cc3..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py +++ /dev/null @@ -1,87 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between atoms in the -# protein and a chaperone provided in the supplemental materials section of: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# This is stored in a tabulated force field with a singularity at a distance R. -# -# To calculate the table for interaction between -# ...the chaperone and a hydrophobic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.475 0.0 5.9 1181 -# ...the chaperone and a hydrophilic bead (2004 PNAS paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 6.0 0.0 0.0 5.9 1181 -# ...the chaperone and a hydrophobic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.60 3.1 8.0 981 True -# ...the chaperone and a hydrophilic bead (2006 JMB paper), use this table: -# ./calc_chaperone_table.py 1.0 1.0 3.0 0.0 3.1 8.0 981 True - -from math import * -import sys - -def U(r, eps, sigma, R, h): - #print('r='+str(r)+' eps='+str(eps)+' s='+str(sigma)+' R='+str(R)+' h='+str(h)) - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 4.0*pi*R*R*4.0*eps*(pow((sigma/R), 12.0) - - h*pow((sigma/R), 6.0)) - xp = sigma/(r+R) - xm = sigma/(r-R) - term10 = pow(xm, 10.0) - pow(xp, 10.0) - term4 = pow(xm, 4.0) - pow(xp, 4.0) - return 4.0*pi*eps*(R/r) * (0.2*term10 - 0.5*h*term4) - -def F(r, eps, sigma, R, h): - # Formula is undefined at r=0, but you can take the limit: - if r <= 0: - return 0.0 - product_term_a = U(r, eps, sigma, R, h) / r - ixp = (r+R)/sigma - ixm = (r-R)/sigma - dix_dr = 1.0/sigma - term10 = (10.0/sigma)*(pow(ixm, -11.0) - pow(ixp, -11.0)) - term4 = (4.0/sigma)*(pow(ixm, -5.0) - pow(ixp, -5.0)) - product_term_b = 4.0*eps*pi*(R/r) * (0.2*term10 - 0.5*h*term4) - return product_term_a + product_term_b - - -class InputError(Exception): - """ A generic exception object containing a string for error reporting. - - """ - def __init__(self, err_msg): - self.err_msg = err_msg - def __str__(self): - return self.err_msg - def __repr__(self): - return str(self) - -if len(sys.argv) < 8: - sys.stderr.write("Error: expected 7 arguments:\n" - "\n" - "Usage: "+sys.argv[0]+" epsilon sigma R h rmin rmax N\n\n") - sys.exit(-1) - -epsilon = float(sys.argv[1]) -sigma = float(sys.argv[2]) -R = float(sys.argv[3]) -h = float(sys.argv[4]) -rmin = float(sys.argv[5]) -rmax = float(sys.argv[6]) -N = int(sys.argv[7]) - -subtract_Urcut = False -if len(sys.argv) == 9: - subtract_Urcut = True -rcut = rmax - -for i in range(0,N): - r = rmin + i*(rmax-rmin)/(N-1) - U_r = U(r, epsilon, sigma, R, h) - F_r = F(r, epsilon, sigma, R, h) - if subtract_Urcut: - U_r -= U(rcut, epsilon, sigma, R, h) - if (r >= rcut) or (i==N-1): - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d8781c26f5..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt +++ /dev/null @@ -1,45 +0,0 @@ -write_once("Data Boundary") { - 0.0 20.0 xlo xhi - 0.0 20.0 ylo yhi - 0.0 20.0 zlo zhi -} - - -import "chaperonin.lt" -import "1beadUnfrustrated_variants.lt" - - -chaperinin = new Chaperonin # (hollow chaperonin, encloses protein) -protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) - - - -# Now define interactions between the "c" atom in the -# chaperone and the "B", "L", "N" atoms in the protein: - -write_once("In Settings") { - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/L table table_chaperonin_h=0.dat CH_H0 - pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/N table table_chaperonin_h=0.dat CH_H0 - # Note: In this example, the chaperone is playing the role of a repulsive wall - # (confinement). To use a sticky chaperonin, replace the first line with this: - # pair_coeff @atom:Chaperonin/C @atom:1beadUnfrustrated/B table table_chaperonin_h=0.475.dat CH_H0.475 -} - - - -# LAMMPS has many available force field styles (and atom styles). -# Here, we pick the ones which work well for this molecular model: - -write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 table spline 1181 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) -} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat deleted file mode 100644 index 675d228a90..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat +++ /dev/null @@ -1,1188 +0,0 @@ -# Interaction between a chaperonin wall and hydrophobic ("B") beads (h=0.475). -# LAMMPS would crash unless I set the minimum radius to a positive value (not 0) - -CH_H0.475 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 -0.018422088583 0.0 -2 0.005 -0.0184221525389 2.55824082873e-05 -3 0.01 -0.0184223444081 5.11654127471e-05 -4 0.015 -0.018422664195 7.67496107175e-05 -5 0.02 -0.0184231119071 0.000102335598797 -6 0.025 -0.018423687555 0.000127923973785 -7 0.03 -0.0184243911519 0.000153515332637 -8 0.035 -0.0184252227143 0.000179110272379 -9 0.04 -0.0184261822615 0.000204709390236 -10 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b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat deleted file mode 100644 index 2ad6d7b691..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat +++ /dev/null @@ -1,1187 +0,0 @@ -# Interaction between a chaperonin wall and hydrophilic beads (type L or N, h=0) - -CH_H0 -N 1181 R 0.00000000001 5.9 - -1 0.00000000001 8.31299178857e-07 0.0 -2 0.005 8.31311879342e-07 -5.08022586688e-09 -3 0.01 8.31349981758e-07 -1.01608369733e-08 -4 0.015 8.31413488996e-07 -1.52422186449e-08 -5 0.02 8.31502405871e-07 -2.03247562721e-08 -6 0.025 8.31616739127e-07 -2.54088353865e-08 -7 0.03 8.31756497437e-07 -3.04948417048e-08 -8 0.035 8.319216914e-07 -3.55831611709e-08 -9 0.04 8.32112333547e-07 -4.06741800058e-08 -10 0.045 8.32328438343e-07 -4.57682847516e-08 -11 0.05 8.32570022183e-07 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-2.55154000294e+12 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt deleted file mode 100644 index 5fb8d71b39..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt +++ /dev/null @@ -1,48 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -# Keep the chaperonin fixed. Only let the protein move. - -fix fxlan proteins langevin 0.39 0.39 1.0 48279 -fix fxnve proteins nve - -# Notes: -# The temperature is in reduced units and is set to 0.39 -# which is the folding temperature for the unfrustrated protein. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 5000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT deleted file mode 100644 index b2770e3e3d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT +++ /dev/null @@ -1,27 +0,0 @@ -# This directory demonstrates how to run a short simulation of -# the "unfrustrated" coarse-grained protein model used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) -# -# During this short simulation (run.in.nvt) the protein evolves -# from an unfolded initial conformation to the folded state. -# -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh deleted file mode 100755 index cb3196cf8a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 1470af4bc1..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,97 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 27 !NATOM - 1 1 2 2 0.000000 1.0000 0 - 2 1 1 1 0.000000 1.0000 0 - 3 1 2 2 0.000000 1.0000 0 - 4 1 1 1 0.000000 1.0000 0 - 5 1 2 2 0.000000 1.0000 0 - 6 1 1 1 0.000000 1.0000 0 - 7 1 3 3 0.000000 1.0000 0 - 8 1 3 3 0.000000 1.0000 0 - 9 1 1 1 0.000000 1.0000 0 - 10 1 2 2 0.000000 1.0000 0 - 11 1 1 1 0.000000 1.0000 0 - 12 1 2 2 0.000000 1.0000 0 - 13 1 1 1 0.000000 1.0000 0 - 14 1 2 2 0.000000 1.0000 0 - 15 1 3 3 0.000000 1.0000 0 - 16 1 3 3 0.000000 1.0000 0 - 17 1 3 3 0.000000 1.0000 0 - 18 1 1 1 0.000000 1.0000 0 - 19 1 1 1 0.000000 1.0000 0 - 20 1 2 2 0.000000 1.0000 0 - 21 1 2 2 0.000000 1.0000 0 - 22 1 1 1 0.000000 1.0000 0 - 23 1 1 1 0.000000 1.0000 0 - 24 1 2 2 0.000000 1.0000 0 - 25 1 2 2 0.000000 1.0000 0 - 26 1 1 1 0.000000 1.0000 0 - 27 1 2 2 0.000000 1.0000 0 - - 26 !NBOND: bonds - 1 2 2 3 3 4 4 5 - 5 6 6 7 7 8 8 9 - 9 10 10 11 11 12 12 13 - 13 14 14 15 15 16 16 17 - 17 18 18 19 19 20 20 21 - 21 22 22 23 23 24 24 25 - 25 26 26 27 - - 25 !NTHETA: angles - 13 14 15 7 8 9 6 7 8 - 16 17 18 15 16 17 2 3 4 - 4 5 6 9 10 11 11 12 13 - 14 15 16 1 2 3 3 4 5 - 10 11 12 12 13 14 25 26 27 - 5 6 7 8 9 10 17 18 19 - 18 19 20 22 23 24 21 22 23 - 19 20 21 20 21 22 23 24 25 - 24 25 26 - - 43 !NPHI: dihedrals - 1 2 3 4 1 2 3 4 - 2 3 4 5 2 3 4 5 - 3 4 5 6 3 4 5 6 - 4 5 6 7 4 5 6 7 - 5 6 7 8 6 7 8 9 - 7 8 9 10 8 9 10 11 - 8 9 10 11 9 10 11 12 - 9 10 11 12 10 11 12 13 - 10 11 12 13 11 12 13 14 - 11 12 13 14 12 13 14 15 - 12 13 14 15 13 14 15 16 - 14 15 16 17 15 16 17 18 - 15 16 17 18 16 17 18 19 - 16 17 18 19 17 18 19 20 - 17 18 19 20 18 19 20 21 - 18 19 20 21 19 20 21 22 - 19 20 21 22 20 21 22 23 - 20 21 22 23 21 22 23 24 - 21 22 23 24 22 23 24 25 - 22 23 24 25 23 24 25 26 - 23 24 25 26 24 25 26 27 - 24 25 26 27 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg deleted file mode 100644 index 152fa88ff9..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg deleted file mode 100644 index bb269f47f2..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt +++ /dev/null @@ -1,255 +0,0 @@ -# This file defines a pair of coarse-grained protein models used in: -# AI Jewett, A Baumketner and J-E Shea, PNAS, 101 (36), 13192-13197, (2004) -# (http://www.pnas.org/content/101/36/13192) - - -1beadUnfrustrated { - - # Note: the "unfrustrated" model is kind of funny looking. (My apologies.) - - # There are 3 atom types (referred to above as B, L, and N) - # Define their masses: - - write_once("Data Masses") { - @atom:B 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -1.3969548 1.7525716 -0.28565118 - $atom:a2 $mol @atom:B 0.0 -0.66847917 1.0738923 -0.39651074 - $atom:a3 $mol @atom:L 0.0 -0.16610379 1.0893417 0.44519456 - $atom:a4 $mol @atom:B 0.0 0.42244126 0.35006314 0.15979926 - $atom:a5 $mol @atom:L 0.0 1.2844393 0.55103218 0.64505356 - $atom:a6 $mol @atom:N 0.0 1.9703715 0.37775946 -0.05267634 - $atom:a7 $mol @atom:N 0.0 2.574926 -0.30399114 0.34330503 - $atom:a8 $mol @atom:N 0.0 2.029546 -1.1256647 0.19829852 - $atom:a9 $mol @atom:B 0.0 1.0936146 -0.76054936 0.1043528 - $atom:a10 $mol @atom:L 0.0 0.74888247 -0.81165991 1.0334863 - $atom:a11 $mol @atom:B 0.0 -0.069536333 -0.26815389 0.94356636 - $atom:a12 $mol @atom:L 0.0 -0.65671052 -0.522532 1.7113065 - $atom:a13 $mol @atom:N 0.0 -1.5278507 -0.10774689 1.4611921 - $atom:a14 $mol @atom:L 0.0 -2.1958878 -0.8403146 1.5521738 - $atom:a15 $mol @atom:N 0.0 -2.6058074 -0.86553455 0.64397232 - $atom:a16 $mol @atom:N 0.0 -1.8447588 -1.1286421 0.042924693 - $atom:a17 $mol @atom:N 0.0 -1.5328721 -0.28576244 -0.40564841 - $atom:a18 $mol @atom:B 0.0 -0.69593879 0.027664412 0.064884008 - $atom:a19 $mol @atom:B 0.0 0.0026517494 -0.66355162 -0.11470678 - $atom:a20 $mol @atom:L 0.0 -0.35479285 -1.2282381 -0.86455878 - $atom:a21 $mol @atom:L 0.0 -0.60202976 -0.47829758 -1.4411001 - $atom:a22 $mol @atom:B 0.0 -0.14616501 0.20157397 -0.87098365 - $atom:a23 $mol @atom:B 0.0 0.7755198 -0.14153019 -0.76838748 - $atom:a24 $mol @atom:L 0.0 1.2465693 0.19738595 -1.5794731 - $atom:a25 $mol @atom:L 0.0 0.77604792 1.0612244 -1.637442 - $atom:a26 $mol @atom:B 0.0 0.44801303 1.1110219 -0.6900789 - $atom:a27 $mol @atom:L 0.0 1.0908651 1.7386382 -0.24229241 - } - - # bond-ID bond-Type atom-ID atom-ID - - write("Data Bonds") { - $bond:b1 @bond:backbone $atom:a1 $atom:a2 - $bond:b2 @bond:backbone $atom:a2 $atom:a3 - $bond:b3 @bond:backbone $atom:a3 $atom:a4 - $bond:b4 @bond:backbone $atom:a4 $atom:a5 - $bond:b5 @bond:backbone $atom:a5 $atom:a6 - $bond:b6 @bond:backbone $atom:a6 $atom:a7 - $bond:b7 @bond:backbone $atom:a7 $atom:a8 - $bond:b8 @bond:backbone $atom:a8 $atom:a9 - $bond:b9 @bond:backbone $atom:a9 $atom:a10 - $bond:b10 @bond:backbone $atom:a10 $atom:a11 - $bond:b11 @bond:backbone $atom:a11 $atom:a12 - $bond:b12 @bond:backbone $atom:a12 $atom:a13 - $bond:b13 @bond:backbone $atom:a13 $atom:a14 - $bond:b14 @bond:backbone $atom:a14 $atom:a15 - $bond:b15 @bond:backbone $atom:a15 $atom:a16 - $bond:b16 @bond:backbone $atom:a16 $atom:a17 - $bond:b17 @bond:backbone $atom:a17 $atom:a18 - $bond:b18 @bond:backbone $atom:a18 $atom:a19 - $bond:b19 @bond:backbone $atom:a19 $atom:a20 - $bond:b20 @bond:backbone $atom:a20 $atom:a21 - $bond:b21 @bond:backbone $atom:a21 $atom:a22 - $bond:b22 @bond:backbone $atom:a22 $atom:a23 - $bond:b23 @bond:backbone $atom:a23 $atom:a24 - $bond:b24 @bond:backbone $atom:a24 $atom:a25 - $bond:b25 @bond:backbone $atom:a25 $atom:a26 - $bond:b26 @bond:backbone $atom:a26 $atom:a27 - } - - # (3-body) Angles are specified below - - # (4-body) Dihedrals must be defined explicitly for every quartet of atoms. - # (These interactions are not determined by atom type.) - # - # Note that some quartets of atoms are listed because their - # potentials contain multiple terms in the Fourier expansion. - # (IE. multiple cosines... Be sure to use "-overlay-dihedrals"!) - # - # dihedral-ID dihedral-Type atom-ID atom-ID atom-ID atom-ID - - write("Data Dihedrals") { - $dihedral:d1a @dihedral:beta1 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d1b @dihedral:beta2 $atom:a1 $atom:a2 $atom:a3 $atom:a4 - $dihedral:d2a @dihedral:beta1 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d2b @dihedral:beta2 $atom:a2 $atom:a3 $atom:a4 $atom:a5 - $dihedral:d3a @dihedral:beta1 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d3b @dihedral:beta2 $atom:a3 $atom:a4 $atom:a5 $atom:a6 - $dihedral:d4a @dihedral:beta1 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d4b @dihedral:beta2 $atom:a4 $atom:a5 $atom:a6 $atom:a7 - $dihedral:d5 @dihedral:turn1 $atom:a5 $atom:a6 $atom:a7 $atom:a8 - $dihedral:d6 @dihedral:turn2 $atom:a6 $atom:a7 $atom:a8 $atom:a9 - $dihedral:d7 @dihedral:turn3 $atom:a7 $atom:a8 $atom:a9 $atom:a10 - $dihedral:d8a @dihedral:beta1 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d8b @dihedral:beta2 $atom:a8 $atom:a9 $atom:a10 $atom:a11 - $dihedral:d9a @dihedral:beta1 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d9b @dihedral:beta2 $atom:a9 $atom:a10 $atom:a11 $atom:a12 - $dihedral:d10a @dihedral:beta1 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d10b @dihedral:beta2 $atom:a10 $atom:a11 $atom:a12 $atom:a13 - $dihedral:d11a @dihedral:beta1 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d11b @dihedral:beta2 $atom:a11 $atom:a12 $atom:a13 $atom:a14 - $dihedral:d12a @dihedral:beta1 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d12b @dihedral:beta2 $atom:a12 $atom:a13 $atom:a14 $atom:a15 - $dihedral:d13 @dihedral:turn4 $atom:a13 $atom:a14 $atom:a15 $atom:a16 - $dihedral:d14 @dihedral:turn5 $atom:a14 $atom:a15 $atom:a16 $atom:a17 - $dihedral:d15a @dihedral:alpha1 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d15b @dihedral:alpha2 $atom:a15 $atom:a16 $atom:a17 $atom:a18 - $dihedral:d16a @dihedral:alpha1 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d16b @dihedral:alpha2 $atom:a16 $atom:a17 $atom:a18 $atom:a19 - $dihedral:d17a @dihedral:alpha1 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d17b @dihedral:alpha2 $atom:a17 $atom:a18 $atom:a19 $atom:a20 - $dihedral:d18a @dihedral:alpha1 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d18b @dihedral:alpha2 $atom:a18 $atom:a19 $atom:a20 $atom:a21 - $dihedral:d19a @dihedral:alpha1 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d19b @dihedral:alpha2 $atom:a19 $atom:a20 $atom:a21 $atom:a22 - $dihedral:d20a @dihedral:alpha1 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d20b @dihedral:alpha2 $atom:a20 $atom:a21 $atom:a22 $atom:a23 - $dihedral:d21a @dihedral:alpha1 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d21b @dihedral:alpha2 $atom:a21 $atom:a22 $atom:a23 $atom:a24 - $dihedral:d22a @dihedral:alpha1 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d22b @dihedral:alpha2 $atom:a22 $atom:a23 $atom:a24 $atom:a25 - $dihedral:d23a @dihedral:alpha1 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d23b @dihedral:alpha2 $atom:a23 $atom:a24 $atom:a25 $atom:a26 - $dihedral:d24a @dihedral:alpha1 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - $dihedral:d24b @dihedral:alpha2 $atom:a24 $atom:a25 $atom:a26 $atom:a27 - } - - # All consecutively bonded triplets of atoms same 3-body bond-angle - # interaction parameters. Of coarse, we could specify them all explicitly - # (as we did for the dihedrals above), but I wanted to show how to specify - # angles by atom type instead. (You can do this for dihedrals & impropers - # also.) - - # angle-Type atom-Type atom-Type atom-Type bond-Type bond-Type - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # (The "*" is a wildcard character. I use "*" to denote any atom-type or - # bond-type which is defined within the current namespace: 1beadUnfrustrated) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:B @atom:B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:B @atom:L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @atom:B @atom:N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @atom:L @atom:N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - } - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond-Type bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 100.0 1.0 - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # angle-Type anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 13.3333333333 105.0 - } - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - # NOTE: Currently, dihedral_coeff charmm does not allow non-integer d - # parameters. I'm hoping this will be fixed eventually. - - write_once("In Settings") { - # Correct version: - #dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57.2957795 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha1 charmm -1.5 1 57 0.0 - # Correct version: - #dihedral_coeff @dihedral:alpha2 charmm 0.375 2 114.591559 0.0 - # Replacing with - dihedral_coeff @dihedral:alpha2 charmm 0.375 2 115 0.0 - dihedral_coeff @dihedral:beta1 charmm -1.5 1 180 0.0 - dihedral_coeff @dihedral:beta2 charmm 0.375 2 360 0.0 - dihedral_coeff @dihedral:turn1 charmm -3.0 1 90 0.0 - # Correct version: - # dihedral_coeff @dihedral:turn2 charmm -3.0 1 11.4591559 0.0 - # Replacing with - dihedral_coeff @dihedral:turn2 charmm -3.0 1 11 0.0 - dihedral_coeff @dihedral:turn3 charmm -3.0 1 -90 0.0 - dihedral_coeff @dihedral:turn4 charmm 0.0 1 0 0.0 - dihedral_coeff @dihedral:turn5 charmm 0.0 1 0 0.0 - } - - write_once("In Settings") { - # Optional: define the atoms in the "proteins" group - group proteins type @atom:B - group proteins type @atom:L - group proteins type @atom:N - } - - # LAMMPS has many available force field styles (and atom styles). - # Here, we pick the ones which work well for this molecular model: - - write_once("In Init") { - # --- Default options for the "1BeadUnfrustrated" protein model --- - # --- (These can be overridden later.) --- - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - -} # 1beadUnfrustrated - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt +++ /dev/null @@ -1,45 +0,0 @@ -import "1beadUnfrustrated.lt" - - -# Alternate starting conformation (same molecule): - - -1beadUnfolded inherits 1beadUnfrustrated { - - # This molecule "inherits" all of its features from "1beadUnfrustrated" - # Here we override the atomic positions with new coordinates: - - # AtomID MoleculeID AtomType Charge X Y Z - - write("Data Atoms") { - $atom:a1 $mol @atom:L 0.0 -2.4 1.7 -0.0 - $atom:a2 $mol @atom:B 0.0 -1.8 1.7 0.8 - $atom:a3 $mol @atom:L 0.0 -1.2 2.5 0.8 - $atom:a4 $mol @atom:B 0.0 -0.6 2.5 -0.0 - $atom:a5 $mol @atom:L 0.0 0.0 1.7 -0.0 - $atom:a6 $mol @atom:B 0.0 0.6 1.7 0.8 - $atom:a7 $mol @atom:N 0.0 1.2 2.5 0.8 - $atom:a8 $mol @atom:N 0.0 1.8 2.5 -0.0 - $atom:a9 $mol @atom:B 0.0 2.4 1.7 -0.0 - $atom:a10 $mol @atom:L 0.0 3.0 1.7 -0.8 - $atom:a11 $mol @atom:B 0.0 3.0 0.7 -0.8 - $atom:a12 $mol @atom:L 0.0 3.0 0.1 -0.0 - $atom:a13 $mol @atom:B 0.0 3.8 -0.5 -0.0 - $atom:a14 $mol @atom:L 0.0 3.8 -1.1 -0.8 - $atom:a15 $mol @atom:N 0.0 3.0 -1.7 -0.8 - $atom:a16 $mol @atom:N 0.0 3.0 -1.7 0.2 - $atom:a17 $mol @atom:N 0.0 2.4 -2.5 0.2 - $atom:a18 $mol @atom:B 0.0 1.8 -2.5 -0.6 - $atom:a19 $mol @atom:B 0.0 1.2 -1.7 -0.6 - $atom:a20 $mol @atom:L 0.0 0.6 -1.7 0.2 - $atom:a21 $mol @atom:L 0.0 -0.0 -2.5 0.2 - $atom:a22 $mol @atom:B 0.0 -0.6 -2.5 -0.6 - $atom:a23 $mol @atom:B 0.0 -1.2 -1.7 -0.6 - $atom:a24 $mol @atom:L 0.0 -1.8 -1.7 0.2 - $atom:a25 $mol @atom:L 0.0 -2.4 -2.5 0.2 - $atom:a26 $mol @atom:B 0.0 -3.0 -2.5 -0.6 - $atom:a27 $mol @atom:L 0.0 -3.6 -1.7 -0.6 - } - -} # 1beadUnfolded - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt deleted file mode 100644 index 5ebe6efb88..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt +++ /dev/null @@ -1,11 +0,0 @@ -import "1beadUnfrustrated_variants.lt" - - -protein = new 1beadUnfolded # (unfolded conformation, unfrustrated protein) - - -write_once("Data Boundary") { - 0.0 27.0 xlo xhi - 0.0 27.0 ylo yhi - 0.0 27.0 zlo zhi -} diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt deleted file mode 100644 index a831a97b4a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.025 -dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.39 0.39 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.39 -# which is the folding temperature for the unfrustrated protein. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0, -# as it was in the paper. (Hopefully folding times should be similar.) -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 50 #(time interval for printing out "thermo" data) - -#restart 100000000 restart_nvt - -run 8000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT deleted file mode 100644 index eda6a1ca22..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README.TXT +++ /dev/null @@ -1,44 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. - -This is an example of a very simple coarse-grained protein. - -This example contains a 1-bead (C-alpha model) representation of the -"unfrustrated" 4-helix bundle model used in this paper: -G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) - -In this model, there are three atom-types (bead-types), H, L, and N -representing one amino-acid each. The "H" beads represent the hydrophobic -amino acids, and are attracted to eachother with a strength of "1.0" -(in dimensionless units of "epsilon"). The "L" and "N" atoms are -hydrophilic and purely repulsive, and only differ in their secondary-structure -propensity (ie their dihedral parameters). - -The dihedral-interaction is bi-stable with two deep local minima (corresponding -to helix-like and sheet-like secondary structure). You can adjust the bias -in favor of one minima or another by modifying the angle-shift parameter in -the appropriate "dihedral_coeff" command in the other .lt file. - -A definition for the 4-sheet beta-barell protein model is also included. -If you want to simulate that molecule instead, then edit the "system.lt" -file (in the "moltemplate_files" subdirectory), and replace this line: -prot = new 4HelixBundle - with -prot = new 4SheetBundle - -------------- -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which refer -# to the input scripts & data files you created earlier when you ran moltemplate -# system.in.init, system.in.settings, system.data - - - - -# ----------------------------------- - - - -LAMMPS_COMMAND="lmp_ubuntu" - -# Here "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -# (such as lmp_linux, lmp_g++, lmp_mac, lmp_cygwin, etc...) Change if necessary. - -# Run lammps using the following 3 commands: - -"$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -"$LAMMPS_COMMAND" -i run.in.nvt # production run - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.min # minimize (OPTIONAL) -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh deleted file mode 100755 index cb3196cf8a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -overlay-dihdedrals system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg deleted file mode 100644 index b4d919f9e6..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg deleted file mode 100644 index cd65146ffa..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index de47509ed4..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,214 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 73 !NATOM - 1 1 1 1 0.000000 1.0000 0 - 2 1 1 1 0.000000 1.0000 0 - 3 1 2 2 0.000000 1.0000 0 - 4 1 2 2 0.000000 1.0000 0 - 5 1 1 1 0.000000 1.0000 0 - 6 1 1 1 0.000000 1.0000 0 - 7 1 2 2 0.000000 1.0000 0 - 8 1 2 2 0.000000 1.0000 0 - 9 1 1 1 0.000000 1.0000 0 - 10 1 1 1 0.000000 1.0000 0 - 11 1 2 2 0.000000 1.0000 0 - 12 1 2 2 0.000000 1.0000 0 - 13 1 1 1 0.000000 1.0000 0 - 14 1 1 1 0.000000 1.0000 0 - 15 1 2 2 0.000000 1.0000 0 - 16 1 2 2 0.000000 1.0000 0 - 17 1 1 1 0.000000 1.0000 0 - 18 1 1 1 0.000000 1.0000 0 - 19 1 2 2 0.000000 1.0000 0 - 20 1 2 2 0.000000 1.0000 0 - 21 1 1 1 0.000000 1.0000 0 - 22 1 1 1 0.000000 1.0000 0 - 23 1 2 2 0.000000 1.0000 0 - 24 1 2 2 0.000000 1.0000 0 - 25 1 1 1 0.000000 1.0000 0 - 26 1 1 1 0.000000 1.0000 0 - 27 1 2 2 0.000000 1.0000 0 - 28 1 2 2 0.000000 1.0000 0 - 29 1 1 1 0.000000 1.0000 0 - 30 1 1 1 0.000000 1.0000 0 - 31 1 2 2 0.000000 1.0000 0 - 32 1 2 2 0.000000 1.0000 0 - 33 1 1 1 0.000000 1.0000 0 - 34 1 1 1 0.000000 1.0000 0 - 35 1 2 2 0.000000 1.0000 0 - 36 1 2 2 0.000000 1.0000 0 - 37 1 1 1 0.000000 1.0000 0 - 38 1 1 1 0.000000 1.0000 0 - 39 1 2 2 0.000000 1.0000 0 - 40 1 2 2 0.000000 1.0000 0 - 41 1 1 1 0.000000 1.0000 0 - 42 1 1 1 0.000000 1.0000 0 - 43 1 2 2 0.000000 1.0000 0 - 44 1 2 2 0.000000 1.0000 0 - 45 1 1 1 0.000000 1.0000 0 - 46 1 1 1 0.000000 1.0000 0 - 47 1 2 2 0.000000 1.0000 0 - 48 1 2 2 0.000000 1.0000 0 - 49 1 1 1 0.000000 1.0000 0 - 50 1 1 1 0.000000 1.0000 0 - 51 1 2 2 0.000000 1.0000 0 - 52 1 2 2 0.000000 1.0000 0 - 53 1 1 1 0.000000 1.0000 0 - 54 1 1 1 0.000000 1.0000 0 - 55 1 2 2 0.000000 1.0000 0 - 56 1 2 2 0.000000 1.0000 0 - 57 1 1 1 0.000000 1.0000 0 - 58 1 1 1 0.000000 1.0000 0 - 59 1 2 2 0.000000 1.0000 0 - 60 1 2 2 0.000000 1.0000 0 - 61 1 1 1 0.000000 1.0000 0 - 62 1 1 1 0.000000 1.0000 0 - 63 1 2 2 0.000000 1.0000 0 - 64 1 2 2 0.000000 1.0000 0 - 65 1 3 3 0.000000 1.0000 0 - 66 1 3 3 0.000000 1.0000 0 - 67 1 3 3 0.000000 1.0000 0 - 68 1 3 3 0.000000 1.0000 0 - 69 1 3 3 0.000000 1.0000 0 - 70 1 3 3 0.000000 1.0000 0 - 71 1 3 3 0.000000 1.0000 0 - 72 1 3 3 0.000000 1.0000 0 - 73 1 3 3 0.000000 1.0000 0 - - 72 !NBOND: bonds - 1 2 2 3 3 4 4 5 - 5 6 6 7 7 8 8 9 - 9 10 10 11 11 12 12 13 - 13 14 14 15 15 16 16 65 - 17 18 17 70 18 19 19 20 - 20 21 21 22 22 23 23 24 - 24 25 25 26 26 27 27 28 - 28 29 29 30 30 31 31 32 - 32 67 33 34 33 68 34 35 - 35 36 36 37 37 38 38 39 - 39 40 40 41 41 42 42 43 - 43 44 44 45 45 46 46 47 - 47 48 48 71 49 50 50 51 - 51 52 52 53 53 54 54 55 - 55 56 56 57 57 58 58 59 - 59 60 60 61 61 62 62 63 - 63 64 64 73 65 66 66 67 - 68 69 69 70 71 72 72 73 - - 71 !NTHETA: angles - 16 65 66 32 67 66 48 71 72 - 64 73 72 2 3 4 3 4 5 - 6 7 8 7 8 9 10 11 12 - 11 12 13 14 15 16 18 19 20 - 19 20 21 22 23 24 23 24 25 - 26 27 28 27 28 29 30 31 32 - 34 35 36 35 36 37 38 39 40 - 39 40 41 42 43 44 43 44 45 - 46 47 48 50 51 52 51 52 53 - 54 55 56 55 56 57 58 59 60 - 59 60 61 62 63 64 15 16 65 - 31 32 67 47 48 71 63 64 73 - 34 33 68 18 17 70 1 2 3 - 4 5 6 5 6 7 8 9 10 - 9 10 11 12 13 14 13 14 15 - 17 18 19 20 21 22 21 22 23 - 24 25 26 25 26 27 28 29 30 - 29 30 31 33 34 35 36 37 38 - 37 38 39 40 41 42 41 42 43 - 44 45 46 45 46 47 49 50 51 - 52 53 54 53 54 55 56 57 58 - 57 58 59 60 61 62 61 62 63 - 17 70 69 33 68 69 65 66 67 - 68 69 70 71 72 73 - - 122 !NPHI: dihedrals - 4 5 6 7 8 9 10 11 - 12 13 14 15 20 21 22 23 - 24 25 26 27 28 29 30 31 - 36 37 38 39 40 41 42 43 - 44 45 46 47 52 53 54 55 - 56 57 58 59 60 61 62 63 - 2 3 4 5 6 7 8 9 - 10 11 12 13 18 19 20 21 - 22 23 24 25 26 27 28 29 - 34 35 36 37 38 39 40 41 - 42 43 44 45 50 51 52 53 - 54 55 56 57 58 59 60 61 - 3 4 5 6 1 2 3 4 - 7 8 9 10 5 6 7 8 - 11 12 13 14 9 10 11 12 - 13 14 15 16 19 20 21 22 - 17 18 19 20 23 24 25 26 - 21 22 23 24 27 28 29 30 - 25 26 27 28 29 30 31 32 - 35 36 37 38 33 34 35 36 - 39 40 41 42 37 38 39 40 - 43 44 45 46 41 42 43 44 - 45 46 47 48 51 52 53 54 - 49 50 51 52 55 56 57 58 - 53 54 55 56 59 60 61 62 - 57 58 59 60 61 62 63 64 - 4 5 6 7 8 9 10 11 - 12 13 14 15 20 21 22 23 - 24 25 26 27 28 29 30 31 - 36 37 38 39 40 41 42 43 - 44 45 46 47 52 53 54 55 - 56 57 58 59 60 61 62 63 - 2 3 4 5 6 7 8 9 - 10 11 12 13 18 19 20 21 - 22 23 24 25 26 27 28 29 - 34 35 36 37 38 39 40 41 - 42 43 44 45 50 51 52 53 - 54 55 56 57 58 59 60 61 - 3 4 5 6 1 2 3 4 - 7 8 9 10 5 6 7 8 - 11 12 13 14 9 10 11 12 - 13 14 15 16 19 20 21 22 - 17 18 19 20 23 24 25 26 - 21 22 23 24 27 28 29 30 - 25 26 27 28 29 30 31 32 - 35 36 37 38 33 34 35 36 - 39 40 41 42 37 38 39 40 - 43 44 45 46 41 42 43 44 - 45 46 47 48 51 52 53 54 - 49 50 51 52 55 56 57 58 - 53 54 55 56 59 60 61 62 - 57 58 59 60 61 62 63 64 - 68 69 70 17 33 68 69 70 - 65 66 67 32 16 65 66 67 - 71 72 73 64 48 71 72 73 - 34 33 68 69 18 17 70 69 - 68 33 34 35 70 17 18 19 - 15 16 65 66 31 32 67 66 - 47 48 71 72 63 64 73 72 - 14 15 16 65 30 31 32 67 - 46 47 48 71 62 63 64 73 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index 9b4ff25354..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,274 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - write_once("In Init") { - units lj - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4SheetBarrel { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, -6) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, -6) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, -6) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, -6) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,6.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-6.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,6.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, -4.5) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, -4.5) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, -4.5) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, -4.5) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,5.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-4.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,5.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - } - # Interactions between different atoms use "repulsive wins" mixing rules - - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # We use the same bond-angle forces whenever - # there are 3 consecutively-bonded atoms: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - - - # From the Bellesia et al 2010 paper: - # for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta)) - # for turns: U_{dih}(\phi) = 0.2*cos(3\phi) - # - # General formula used for "dihedral_style fourier": - # U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ] - # - # Syntax: - # dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ... - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - } - # Note: This next rule is not needed: - # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - # (By reflection symmetry, it's equivalent to the rule above.) - # - # Note: The example in ../../membrane+protein/moltemplate_files/ - # demonstrates how to define dihedral angles for this model - # in an alternate way which might be easier to understand. - - - # --- Mass Units --- - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses (in reduced units): - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - } - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh deleted file mode 100755 index 852b9b76f2..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh +++ /dev/null @@ -1,13 +0,0 @@ -# run moltemplate this way - -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data -# which are needed by LAMMPS. - -# ------ Other versions: -------- -# -# If you are using the "other_versions/charmm/1beadProtSci2010.lt" file, -# then you must run moltemplate this way: -# -# moltemplate.sh -overlay-dihdedrals system.lt diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT deleted file mode 100644 index 82bc8c5c43..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/README.TXT +++ /dev/null @@ -1,13 +0,0 @@ -This directory contains other versions of the same molecule -(with the same force-field), implemented in different ways. - -charmm/1beadProtSci2010.lt <-- This applies multiple "charmm" dihedral angle - forces to the same quartet of atoms to create - a Fourier series. (No packages needed.) - - NOTE: You must run moltemplate this way: - - moltemplate.sh -overlay-dihdedrals system.lt - -class2/1beadProtSci2010.lt <-- This uses the "class2" dihedral angles forces - (You must build LAMMPS with the CLASS2 package) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt deleted file mode 100644 index d57186bee7..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/charmm/1beadProtSci2010.lt +++ /dev/null @@ -1,411 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# -# For portability, all definitions in this file are enclosed within -# the "1beadProtSci2010" namespace. To access them, put -# "using namespace 1beadProtSci2010" in your LT file. - -# Strategy: -# -#1) First I'll define some building blocks -# (short helices, sheets and turns of a predetermined length) -# -#2) Then I'll cut and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# -# Doing it this way is optional. It's simpler (but longer) to simply write -# out the entire sequence of all 73 atoms in a single "Data Atoms" section. -# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the -# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions -# manually (instead of inferring them from the atom type). If your protein -# has helices which are not identical, this would probably be easier. -# Use whichever style you prefer. -# -# -# Note that atom types, bond types, angle types, and dihedral types -# are shared between all molecules defined in the "1beadProtSci2010" family. -# (That's why there is a "../" in their path-names. Otherwise atom, bond, -# angle types, etc... are not shared between different molecules.) -# -# Confusing detail: -# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). -# These are represented by the "$mol" variable written next to each atom. -# Our protein has multiple subunits (in this case: helices, sheets, turns). -# Because we want the subunits to share the same molecule-ID counter we use -# "$mol:..." instead of "$mol" which tells moltemplate to search for the -# parent molecule's ID. This is optional. If it bothers you, just use "$mol" - - - -1beadProtSci2010 { - - write_once("In Init") { - # -- Default styles for "1beadProtSci2010" -- - units lj - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 4.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # ---- Building blocks: A16, B16, Turn3 ---- - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) - # can be shared. The ".." in "@atom:../CA" tells moltemplate that - # atom type CA is defined in the parent's environment. (We are - # sharing the CA atom type between both the H and P residues. - # The same is true of the ".." in "@bond:../sidechain". - # - # - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # molecule's id number as it's own. - - - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) - # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) - - # Note: In the paper, this is described as the "UA2" conformation - # (I played around with the angles until it looked "okay". This is not - # the minimum energy conformation. Further minimization is necessary.) - - # Now bond the pieces together. - # (Note: angle & dihedral interactions will be generated automatically.) - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # <-- create a variable for the parent's Molecule-ID - } - - 4SheetBundle { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) - # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses: - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - - } - - - - # -------------------------------------------------------------------- - # -- In this example, all force field parameters are stored in the -- - # -- file named "In Settings". They can also go in sections like -- - # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- - # -------------------------------------------------------------------- - - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 - } - # (Interactions between different atom types use "arithmetic" - # and "maxmax" ("repulsion-wins") mixing rules.) - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType bondstylename k r0 - # - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # The corresponding command is: - # - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded - # together. We do this by to asking moltemplate to generate this - # 3-body interaction whenever 3 consecutively bonded atoms satisfy - # the following type requirement: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone * * * * * - } - - - - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - # dihedral_coeff dihedralType dihedralstylename K n d w - # ("w" is the weight for 1-4 pair interactions, which we set to 0) - - write_once("In Settings") { - dihedral_coeff @dihedral:turn charmm 0.2 3 0 0 - dihedral_coeff @dihedral:term3 charmm 1.2 3 0 0 - - dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65 0 - dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62 0 - dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60 0 - dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57 0 - dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55 0 - } - - #write_once("In Settings") { - # dihedral_coeff @dihedral:turn charmm 0.2 3 0.0 0 - # dihedral_coeff @dihedral:term3 charmm 1.2 3 0.0 0 - # dihedral_coeff @dihedral:delta65_0 charmm 1.2 1 -65.0 0 - # dihedral_coeff @dihedral:delta62_5 charmm 1.2 1 -62.5 0 - # dihedral_coeff @dihedral:delta60_0 charmm 1.2 1 -60.0 0 - # dihedral_coeff @dihedral:delta57_5 charmm 1.2 1 -57.5 0 - # dihedral_coeff @dihedral:delta55_0 charmm 1.2 1 -55.5 0 - #} - - # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy - # the following type requirements: - - write_once("Data Dihedrals By Type") { - # The dihedral interaction between backbone atoms in the helix or sheet-like - # regions is proportional to the sum of two terms: cos(phi+delta)+cos(3*phi) - # where delta is a constant used to control the bias between helices/sheets. - # As of 2013-4-07, the "fourier", "table", "class2", and "charmm", - " dihedral_styles can implement this potential. - # However dihedral_style "charmm" can only handle one cosine term at a time. - # So we use two commands to create two dihedral interactions for the same - # set of of four atoms ("cos3" and "delta60_0"). (To allow the - # superposition of multiple dihedral interactions on the same atoms, - # be sure to run moltemplate with the "-overlay-dihdedrals" argument.) - # - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - @dihedral:term3 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - - @dihedral:term3 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - - @dihedral:term3 @atom:L @atom:H @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - - @dihedral:term3 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - - # Comment out the next 4 lines: (They are redundant with the lines above) - #@dihedral:term3 @atom:L @atom:L @atom:H @atom:H * * * - #@dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * - #@dihedral:term3 @atom:L @atom:H @atom:L @atom:H * * * - #@dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * - # (Redundant: The LLHH pattern is identical to HHLL after order reversal) - # (Redundant: The LHLH pattern is identical to HLHL after order reversal) - - # Right now the dihedral-angle settings are "unfrustrated", meaning that the - # peptide backbone is equally happy to adopt helical or sheet-like secondary - # structure (See Table IV of Bellesia et. al, Prot Sci, 19, 141 (2010)). - # You can change that by changing "delta60_0" to one of the other choices. - - # Any dihedral interactions containing "N" atoms use the @dihedral:turn - # interaction (which is much weaker). - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - # Comment out the next 4 lines: (They are redundant with the lines above) - # @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * - # @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt deleted file mode 100644 index a0e305f844..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/other_implementations/class2/1beadProtSci2010.lt +++ /dev/null @@ -1,385 +0,0 @@ -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -# -# -# For portability, all definitions in this file are enclosed within -# the "1beadProtSci2010" namespace. To access them, put -# "using namespace 1beadProtSci2010" in your LT file. - -# Strategy: -# -#1) First I'll define some building blocks -# (short helices, sheets and turns of a predetermined length) -# -#2) Then I'll cut and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. -# -# Doing it this way is optional. It's simpler (but longer) to simply write -# out the entire sequence of all 73 atoms in a single "Data Atoms" section. -# (IE. Don't try to subdivide it.) It's also simpler to explicitly list the -# 72 bonds, 71 3-body angles and 70 4-body dihedral angle interactions -# manually (instead of inferring them from the atom type). If your protein -# has helices which are not identical, this would probably be easier. -# Use whichever style you prefer. -# -# -# Note that atom types, bond types, angle types, and dihedral types -# are shared between all molecules defined in the "1beadProtSci2010" family. -# (That's why there is a "../" in their path-names. Otherwise atom, bond, -# angle types, etc... are not shared between different molecules.) -# -# Confusing detail: -# Each molecule in LAMMPS can be assigned a unique molecule-ID (an integer). -# These are represented by the "$mol" variable written next to each atom. -# Our protein has multiple subunits (in this case: helices, sheets, turns). -# Because we want the subunits to share the same molecule-ID counter we use -# "$mol:..." instead of "$mol" which tells moltemplate to search for the -# parent molecule's ID. This is optional. If it bothers you, just use "$mol" - - - -1beadProtSci2010 { - - write_once("In Init") { - # -- Default styles for "1beadProtSci2010" -- - units lj - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid class2 - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 3.5 4.0 rsoftcore 1 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 4.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 3.5 4.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - - # ---- Building blocks: A16, B16, Turn3 ---- - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.4 -0.4 0.0 - $atom:a2 $mol:... @atom:../L 0.0 0.4 -0.4 0.6 - $atom:a3 $mol:... @atom:../H 0.0 0.4 0.4 1.2 - $atom:a4 $mol:... @atom:../H 0.0 -0.4 0.4 1.8 - $atom:a5 $mol:... @atom:../L 0.0 -0.4 -0.4 2.4 - $atom:a6 $mol:... @atom:../L 0.0 0.4 -0.4 3.0 - $atom:a7 $mol:... @atom:../H 0.0 0.4 0.4 3.6 - $atom:a8 $mol:... @atom:../H 0.0 -0.4 0.4 4.2 - $atom:a9 $mol:... @atom:../L 0.0 -0.4 -0.4 4.8 - $atom:a10 $mol:... @atom:../L 0.0 0.4 -0.4 5.4 - $atom:a11 $mol:... @atom:../H 0.0 0.4 0.4 6.0 - $atom:a12 $mol:... @atom:../H 0.0 -0.4 0.4 6.6 - $atom:a13 $mol:... @atom:../L 0.0 -0.4 -0.4 7.2 - $atom:a14 $mol:... @atom:../L 0.0 0.4 -0.4 7.8 - $atom:a15 $mol:... @atom:../H 0.0 0.4 0.4 8.4 - $atom:a16 $mol:... @atom:../H 0.0 -0.4 0.4 9.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../L 0.0 -0.3 0.0 0.0 - $atom:a2 $mol:... @atom:../H 0.0 0.3 0.0 0.8 - $atom:a3 $mol:... @atom:../L 0.0 -0.3 0.0 1.6 - $atom:a4 $mol:... @atom:../H 0.0 0.3 0.0 2.4 - $atom:a5 $mol:... @atom:../L 0.0 -0.3 0.0 3.2 - $atom:a6 $mol:... @atom:../H 0.0 0.3 0.0 4.0 - $atom:a7 $mol:... @atom:../L 0.0 -0.3 0.0 4.8 - $atom:a8 $mol:... @atom:../H 0.0 0.3 0.0 5.6 - $atom:a9 $mol:... @atom:../L 0.0 -0.3 0.0 6.4 - $atom:a10 $mol:... @atom:../H 0.0 0.3 0.0 7.2 - $atom:a11 $mol:... @atom:../L 0.0 -0.3 0.0 8.0 - $atom:a12 $mol:... @atom:../H 0.0 0.3 0.0 8.8 - $atom:a13 $mol:... @atom:../L 0.0 -0.3 0.0 9.6 - $atom:a14 $mol:... @atom:../H 0.0 0.3 0.0 10.4 - $atom:a15 $mol:... @atom:../L 0.0 -0.3 0.0 11.2 - $atom:a16 $mol:... @atom:../H 0.0 0.3 0.0 12.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../N 0.0 -0.8 0.0 0.0 - $atom:a2 $mol:... @atom:../N 0.0 0.0 0.55 -0.24 - $atom:a3 $mol:... @atom:../N 0.0 0.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) - # can be shared. The ".." in "@atom:../CA" tells moltemplate that - # atom type CA is defined in the parent's environment. (We are - # sharing the CA atom type between both the H and P residues. - # The same is true of the ".." in "@bond:../sidechain". - # - # - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # molecule's id number as it's own. - - - - # ----- Now build larger molecules using A16, B16 and T3 ------- - - 4HelixBundle { - - helix1 = new A16.rot( -45, 0,0,1).move(-1.12691645,-1.12691645, 0) - helix2 = new A16.rot( 45, 0,0,1).move( 1.12691645,-1.12691645, 0) - helix3 = new A16.rot( 135, 0,0,1).move( 1.12691645, 1.12691645, 0) - helix4 = new A16.rot( 225, 0,0,1).move(-1.12691645, 1.12691645, 0) - # Note: 1.12691645 ~= 0.5*2^(1/6) + 0.4*sqrt(2) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-0.2,-0.7,9.9) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(0.7,-0.15,-0.3) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(0.2,0.7,9.9) - - # Note: In the paper, this is described as the "UA2" conformation - # (I played around with the angles until it looked "okay". This is not - # the minimum energy conformation. Further minimization is necessary.) - - # Now bond the pieces together. - # (Note: angle & dihedral interactions will be generated automatically.) - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # <-- create a variable for the parent's Molecule-ID - } - - 4SheetBundle { - - sheet1 = new B16.rot( 45, 0,0,1).move(-0.793700526,-0.793700526, 0) - sheet2 = new B16.rot( 135, 0,0,1).move( 0.793700526,-0.793700526, 0) - sheet3 = new B16.rot( 225, 0,0,1).move( 0.793700526, 0.793700526, 0) - sheet4 = new B16.rot( 315, 0,0,1).move(-0.793700526, 0.793700526, 0) - # Note: 0.793700526 ~= 0.5*2^(1/6) * sqrt(1/2) - - turn1 = new T3.rot(180,1,0,0).rot(0,0,0,1).move(0,-1.3,12.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(0.7,-0.0,-0.9) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move(0,1.3,12.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # There are 3 atom types (referred to above as ../H, ../L, and ../N) - # Define their masses: - - write_once("Data Masses") { - @atom:H 1.0 - @atom:L 1.0 - @atom:N 1.0 - - } - - - - # -------------------------------------------------------------------- - # -- In this example, all force field parameters are stored in the -- - # -- file named "In Settings". They can also go in sections like -- - # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- - # -------------------------------------------------------------------- - - - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:H @atom:H lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 0 0 0 0 - pair_coeff @atom:L @atom:L lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 - pair_coeff @atom:N @atom:N lj/charmm/coul/charmm/inter 1.0 1.0 1 0 0 0 0 0 - } - # (Interactions between different atom types use "arithmetic" - # and "maxmax" ("repulsion-wins") mixing rules.) - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType bondstylename k r0 - # - - write_once("In Settings") { - bond_coeff @bond:backbone harmonic 66.6 1.0 - } - - - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # The corresponding command is: - # - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 66.6 105.0 - } - - # Generate a "backbone" 3-body interaction whenever 3 atoms are bonded - # together. We do this by to asking moltemplate to generate this - # 3-body interaction whenever 3 consecutively bonded atoms satisfy - # the following type requirement: - # - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone * * * * * - } - - - - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is: - # - - # From the Bellesia et al paper: Udihedral(x) = 1.2*(cos(x+delta) + cos(3x)) (delta=60) - # (scratchwork: 1.2*cos(x+60) = -1.2*cos(x+60-180) = -1.2*cos(x-120)) - # and 1.2*cos(3x) = -1.2*cos(3x-180) - # and 0.2*cos(x) = -0.2*cos(x - 180) - # This way, the energies match exactly with the implementation using charmm dihedrals.) - # - # dihedralType dihedralstylename K1 phi1 K2 phi2 K3 phi3 - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 class2 1.2 120.0 0 0 1.2 180.0 - dihedral_coeff @dihedral:turn class2 0 0 0 0 0.2 180.0 - - # All of the cross-terms (for the class2 force-field) are zero (see docs): - dihedral_coeff @dihedral:delta60_0 class2 mbt 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 ebt 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 at 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 aat 0 0 0 - dihedral_coeff @dihedral:delta60_0 class2 bb13 0 0 0 - dihedral_coeff @dihedral:turn class2 mbt 0 0 0 0 - dihedral_coeff @dihedral:turn class2 ebt 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:turn class2 at 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:turn class2 aat 0 0 0 - dihedral_coeff @dihedral:turn class2 bb13 0 0 0 - } - - # Generate 4-body interactions whenever 4 consecutively bonded atoms satisfy - # the following type requirements: - - write_once("Data Dihedrals By Type") { - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - @dihedral:delta60_0 @atom:H @atom:L @atom:H @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:H @atom:L @atom:L * * * - @dihedral:delta60_0 @atom:H @atom:L @atom:L @atom:H * * * - @dihedral:delta60_0 @atom:L @atom:H @atom:H @atom:L * * * - - @dihedral:turn @atom:N @atom:* @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:* @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:* * * * - @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - - #### Comment out the next 6 lines: (They are redundant with the lines above) - ## @dihedral:delta60_0 @atom:L @atom:H @atom:L @atom:H * * * - ## @dihedral:delta60_0 @atom:L @atom:L @atom:H @atom:H * * * - ## @dihedral:turn @atom:N @atom:N @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:N @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:* @atom:N @atom:N * * * - ## @dihedral:turn @atom:* @atom:* @atom:* @atom:N * * * - ################################################################### - } - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt deleted file mode 100644 index fcc6188f71..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt +++ /dev/null @@ -1,25 +0,0 @@ -import "1beadProtSci2010.lt" - -using namespace 1beadProtSci2010 - -prot = new 4HelixBundle - -write_once("Data Boundary") { - 0 100 xlo xhi - 0 100 ylo yhi - 0 100 zlo zhi -} - - - - -# ------------ Note: ------------- -# -# If you want to try the version using "CHARMM" dihedrals, import this instead: -# -# import "versions_with_comments/1beadProtSci2010_charmm.lt" -# -# (The two versions should behave identically. However by overlaying -# dihedral interactions on top of eachother, charmm allows you to construct -# a Fourier series with an arbitrary number of terms. Class2 stops at 3. -# This is useful if one day you want to use a more complex dihedral potential.) diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.min +++ /dev/null @@ -1,19 +0,0 @@ -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -minimize 1.0e-5 1.0e-7 500 2000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt deleted file mode 100644 index f1a7aa6540..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/run.in.nvt +++ /dev/null @@ -1,44 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.008 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 0.4 0.4 1.0 48279 -fix fxnve all nve - -# Notes: -# The temperature is in reduced units and is set to 0.4. -# The inverse-damping-rate "damp" (which has units of time) is set to 1.0. -# (See http://lammps.sandia.gov/doc/fix_langevin.html) - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo_modify norm no #(report total energy not energy / num_atoms) -thermo 500 #(time interval for printing out "thermo" data) - -restart 10000000 restart_nvt - -run 1000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT deleted file mode 100644 index 305d00d636..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README.TXT +++ /dev/null @@ -1,114 +0,0 @@ - This example shows how to build a multicomponent spherical vesicle. - The lipid bilayer is composed of two different lipids (DPPC and DLPC). - The vesicle also contains trans-membrane protein inclusions. - - The coordinates for the vesicle are constructed by PACKMOL (see below). - - The DPPC lipid model is described here: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) - (The DLPC model is a truncated version of DPPC. Modifications discussed below.) - The protein model is described here: - G. Bellesia, AI Jewett, and J-E Shea, - Protein Science, Vol19 141-154 (2010) - ---- PREREQUISITES: --- - -1) This example requires PACKMOL. You can download PACKMOL here: - - http://www.ime.unicamp.br/~martinez/packmol/ - - (Moltemplate does not come with an easy way to generate spherically-symmetric - structures, so I used the PACKMOL program to move the molecules into position.) - -2) This example requires the "dihedral_style fourier", which is currently -in the USER-MISC package. Build LAMMPS with this package enabled using - make yes-user-misc -before compiling LAMMPS. -(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.) - -3) This example may require additional features to be added to LAMMPS. -If LAMMPS complains about an "Invalid pair_style", then - a) download the "additional_lammps_code" from - http://moltemplate.org (upper-left corner menu) - b) unpack it - c) copy the .cpp and .h files to the src folding of your lammps installation. - d) (re)compile LAMMPS. - ------- Details ------- - -This example contains a coarse-grained model of a 4-helix bundle protein -inserted into a lipid bilayer (made from a mixture of DPPC and DLPC). - - -- Protein Model: -- - -The coarse-grained protein is described in: - G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010) -Here we use the "AUF2" model described in that paper. -(The hydrophobic beads face outwards.) - - -- Memebrane Model: -- - -The DPPC lipid bilayer described in: - G. Brannigan, P.F. Philips, and F.L.H. Brown, - Physical Review E, Vol 72, 011915 (2005) -and: - M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown - J. Chem. Phys. 135, 244701 (2011) - -As in Watson(JCP 2011), rigid bond-length constraints -have been replaced by harmonic bonds. - -A truncated version of this lipid (named "DLPC") has also been added. -The bending stiffness of each lipid has been increased to compensate -for the additional disorder resulting from mixing two different types -of lipids together. (Otherwise pores appear.) -Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models -have not been carefully parameterized to reproduce the correct behavior in -a lipid bilayer mixture. - - -- Interactions between the proteins and lipids -- - -This is discussed in the "system.lt" file. - ---- Building the files necessary to run a simulation in LAMMPS --- - -step 1) Run PACKMOL - - Type these commands into the shell. - (Each command could take several hours.) - -cd packmol_files - packmol < step1_proteins.inp # This step determines the protein's location - packmol < step2_innerlayer.inp # this step builds the inner monolayer - packmol < step3_outerlayer.inp # this step builds the outer monolayer -cd .. - -step 2) Run MOLTEMPLATE - Type these commands into the shell. - (This could take up to 10 minutes.) - -cd moltemplate_files - moltemplate.sh system.lt -xyz ../system.xyz - mv -f system.in* system.data ../ - cp -f table_int.dat ../ -cd .. - ---- Running LAMMPS --- - -step3) Run LAMMPS: - Type these commands into the shell. - (This could take days.) - -lmp_linux -i run.in.min # Minimize the system (important, and very slow) - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - -If you have compiled the MPI version of lammps, you can run lammps in parallel: - -mpirun -np 4 lmp_linux -i run.in.min - or -mpirun -np 4 lmp_linux -i run.in.nvt - -(Assuming you have 4 cores, for example.) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh deleted file mode 100755 index 99f39891e4..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_run.sh +++ /dev/null @@ -1,24 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with MOLTEMPLATE and PACKMOL: -# system.in.init, system.in.settings, system.in.coords, system.data, -# and table_int.dat -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - -lmp_linux -i run.in.min # Minimize the system (important, and very slow) - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.min -#or -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh deleted file mode 100755 index 0764f02f30..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_setup.sh +++ /dev/null @@ -1,50 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - -# First, generate the coordinates (the "system.xyz" file) this way -# (This can be a very slow process.) -cd packmol_files - - # You must run each packmol commend one after the other - # NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding - # "inp" file. This should not happen. You can also usually interrupt - # packmol after 30 minutes, and the solution at that point should be good - # enough for use. - packmol < step1_proteins.inp # This step determines the protein's location - # It takes ~20 minutes (on an intel i7) - packmol < step2_innerlayer.inp # this step builds the inner monolayer - # It takes ~90 minutes - packmol < step3_outerlayer.inp # this step builds the outer monolayer - # It takes ~4 hours - - # Running these three commands will probably take about an hour. - # (It depends on how uniformly you need the packing to be.) - - mv -f step3_outerlayer.xyz ../system.xyz -cd .. - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt -xyz ../system.xyz - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # The "table_int.dat" file contains tabular data for the lipid INT-INT atom - # 1/r^2 interaction. We need it too. (This slows down the simulation by x2, - # so I might look for a way to get rid of it later.) - cp -f table_int.dat ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg deleted file mode 100644 index 843a8f2d83..0000000000 Binary files a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/images/vesicle_hole_blackbk_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index d2aa805a5b..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,233 +0,0 @@ -# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle (or a 4-strand beta-barrel). -# This approach is optional. If your protein has helices which are not -# identical, you should probably just include all 4 helices in a single -# "Data Atoms" section and don't try to subdivide the protein into pieces.) - - - -1beadProtSci2010 { # <-- enclose definitions in a namespace for portability - - # A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each) - - A16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0 - $atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6 - $atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2 - $atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8 - $atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4 - $atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0 - $atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6 - $atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2 - $atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8 - $atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4 - $atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0 - $atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6 - $atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2 - $atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8 - $atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4 - $atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # A16 - - - T3 { # T3 is a "turn" region consisting of 3 beads - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0 - $atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44 - $atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - } - - } # T3 - - - # ----- Now build a larger molecule using A16 and T3 ------- - - # Create a 4-Helix bundle. - # In this version, the hydrophobic beads are poing outward. - # I oriented them this way because I want to place this protein in a membrane. - # (There is another file in this directory containing alternate version - # of this same molecule with the hydrophobic beads pointing inward.) - - 4HelixInsideOut { - helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6) - - turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9) - turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0) - turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOut - - - # -------- Minor coordinates adjustment: ----------- - - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) - - 4HelixInsideOut.scale(0.9166666666666666) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - - - # -------------- Force-Field Parameters ------------ - - # Units and force-field styles for this protein model - # (These can be overridden later.) - - write_once("In Init") { - units real - atom_style full - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid fourier - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions) - } - - # --- Distance Units --- - # In this version of the model, sigma (the bond-length - # and particle diameter) is rounded to 5.5 Angstroms. - # - # --- Energy & Temperature Units --- - # In this protein model, "epsilon" represents the free energy - # bonus for bringing two hydrophobic amino acids together. - # Here I choose to set epsilon to 1.806551818181818 kCal/mole. - # This value was chosen so that a temperature of 300 Kelvin lies at - # 0.33 epsilon, which is the unfolding temperature of the marginally stable - # "ASF1" protein model from the Bellesia et al 2010 paper. - # This choice insures that both the "ASF1" model from that paper, - # as well as the much more stable "AUF2" protein we use here (which - # unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin, - # in the bulk at least. (However it's not clear that these energy - # parameters will work well for a protein in membrane. Perhaps I'll - # run some tests and fine tune these parameters for this scenario.) - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6) - # - # i j pairstylename eps sig K L - # - write_once("In Settings") { - pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - } - - # The exact value of the bond_coeff does not matter too much as long as - # it is "stiff enough". Here I use a softer bond spring than the one - # used in the paper so that I can increase the time step. - # I also use a relatively soft spring to constrain the bond angles. - - # bond_coeff bondType bondstylename k r0 - - write_once("In Settings") { - bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5 - } - - - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - # angle_coeff angleType anglestylename k theta0 - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 100.0 105.0 - } - - - # dihedralType atomtypes1 2 3 4 bondtypes1 2 3 - - write_once("Data Dihedrals By Type") { - # For a chain of sH and sL atoms, use the @dihedral:delta65_0 - # parameters. (This corresponds to the "AUF2" model from the - # Bellesia et. al 2010 paper.) - - @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * - - # If "tN" (turn) atoms are present, use the @dihedral:turn parameters - - @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * - } - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0 - dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0 - dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - } - - - # --- Mass Units --- - # Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down): - write_once("Data Masses") { - @atom:1beadProtSci2010/sH 100.0 - @atom:1beadProtSci2010/sL 100.0 - @atom:1beadProtSci2010/tN 100.0 - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt deleted file mode 100644 index e6e6bced70..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/1beadProtSci2010_variations.lt +++ /dev/null @@ -1,225 +0,0 @@ -### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ## -### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE## -# -# This file defines a family of coarse-grained protein models used in: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# -# Strategy: -# -#1) First I'll define some building blocks (A16, B16, T3) -# which are helices, sheets and turns of a predetermined length) - -import "1beadProtSci2010.lt" - -# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below -# -#2) Then I'll copy and paste them together to build -# a 4-helix bundle or a 4-strand beta-barrel. - - -1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier - # This way we don't have to start from scratch. We can - # use all the atom types and angle settings defined earlier - - # B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each) - - B16 { - - # AtomID MoleculeID AtomType Charge X Y Z - - write('Data Atoms') { - $atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0 - $atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8 - $atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6 - $atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4 - $atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2 - $atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0 - $atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8 - $atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6 - $atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4 - $atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2 - $atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0 - $atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8 - $atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6 - $atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4 - $atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2 - $atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0 - } - - write('Data Bonds') { - $bond:b1 @bond:../backbone $atom:a1 $atom:a2 - $bond:b2 @bond:../backbone $atom:a2 $atom:a3 - $bond:b3 @bond:../backbone $atom:a3 $atom:a4 - $bond:b4 @bond:../backbone $atom:a4 $atom:a5 - $bond:b5 @bond:../backbone $atom:a5 $atom:a6 - $bond:b6 @bond:../backbone $atom:a6 $atom:a7 - $bond:b7 @bond:../backbone $atom:a7 $atom:a8 - $bond:b8 @bond:../backbone $atom:a8 $atom:a9 - $bond:b9 @bond:../backbone $atom:a9 $atom:a10 - $bond:b10 @bond:../backbone $atom:a10 $atom:a11 - $bond:b11 @bond:../backbone $atom:a11 $atom:a12 - $bond:b12 @bond:../backbone $atom:a12 $atom:a13 - $bond:b13 @bond:../backbone $atom:a13 $atom:a14 - $bond:b14 @bond:../backbone $atom:a14 $atom:a15 - $bond:b15 @bond:../backbone $atom:a15 $atom:a16 - } - - } # B16 - - # ----- Now build larger molecules using B16 and T3 ------- - - - 4SheetBarrel { - sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0) - sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0) - sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0) - sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6) - turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4) - turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # Below I define several alternate conformations of the"4HelixBundleInsideOut" - # molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however. - - 4HelixBundle { - helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4) - helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8) - helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2) - helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - - turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2) - turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9) - turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4) - - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixBundle - - - - - # --- alternate conformations (same molecule) ---- - - # In the following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixBundleLoose { - - helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4) - turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8) - turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - } - - - # In following version, the helices are oriented in a similar way, - # but they are separated a little further away from eachother. - - 4HelixInsideOutLoose { - helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0) - helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0) - helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0) - helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8) - turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2) - turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixInsideOutLoose - - - - - # In the following version, the 4 helices are arranged next to each other, - # side-by-side, in a planar conformation (instead of a compact bundle). - - 4HelixPlanar { - helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0) - helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0) - helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0) - helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0) - - turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8) - turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8) - turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8) - - write('Data Bonds') { - $bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16 - $bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16 - $bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1 - $bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1 - $bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16 - $bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16 - } - create_var { $mol } # molecule ID number shared by all atoms in this protein - - } # 4HelixPlanar - - - # -------- Minor coordinates adjustment: ----------- - # Those coordinates in the commands above are a little too large. - # To make it easier to type them in, I was using sigma=6.0 Angstroms. - # Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667) - - 4SheetBarrel.scale(0.9166666666666666) - 4HelixBundle.scale(0.9166666666666666) - 4HelixBundleLoose.scale(0.9166666666666666) - 4HelixInsideOutLoose.scale(0.9166666666666666) - 4HelixPlanar.scale(0.9166666666666666) - - # Note: "scale()" only effects the initial coordinates of - # the molecule, not the force field parameters. - # (If you plan to minimize the molecule, you don't need to - # be so careful about the initial coordinates. In that case, - # you don't have worry about "scale()". Feel free to remove.) - - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index 3b39048f7e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,198 +0,0 @@ -# Note: -# -# This example may require additional features to be added to LAMMPS. If -# LAMMPS complains about an "Invalid pair_style", then download copy the -# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS -# "src" directory and recompile LAMMPS. -# -# -------- Description -------- -# -# This example contains an implementation of the DPPC lipid bilayer described in -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# and: -# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown -# J. Chem. Phys. 135, 244701 (2011) -# -# As in Watson(JCP 2011), rigid bond-length constraints have been replaced -# by harmonic bonds. -# -# A truncated version of this lipid (named "DLPC") has also been added. -# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully -# parameterized to reproduce the correct behavior in a lipid bilayer mixture. -# -# Units: -# -# The "epsilon" parameter in their model is approximately 2.75 kJ/mole -# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ) -# The "sigma" parameter corresponds to 7.5 angstroms. - - -CGLipidBr2005 { - - - write_once("In Init") { - # -- Default styles for "CGLipidBr2005" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - - #angle_style hybrid cosine/delta # <- used in the original article - angle_style hybrid harmonic # <- prevents unphysical acute angle turns - # Explanation: - # angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - # angle_style harmonic: U(theta) = k*(theta-theta0)^2 - - dihedral_style none - improper_style none - pair_style hybrid table linear 1130 & - lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - neighbor 2.0 multi # <- perhaps unnecessary - communicate multi # <- perhaps unnecessary - } - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25 - $atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - $bond:b4 @bond:../backbone $atom:t2 $atom:t3 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - $angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3 - } - - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - - } #DPPC - - - DLPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom - $atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50 - $atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00 - $atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50 - } - write("Data Bonds") { - $bond:b1 @bond:../backbone $atom:h $atom:i - $bond:b2 @bond:../backbone $atom:i $atom:t1 - $bond:b3 @bond:../backbone $atom:t1 $atom:t2 - } - write("Data Angles") { - $angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1 - $angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2 - } - # Define properties of the local (lipid-specific) atom:head type atom: - write_once("Data Masses") { - @atom:head 200.0 - } - write_once("In Settings") { - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - } - } #DLPC - - - # Particles and properties shared by all lipid types: - - write_once("Data Masses") { - @atom:int 200.0 - @atom:tail 200.0 - @atom:head 200.0 #<- Default head type. We may override it later. - } - - write_once("In Settings") { - # -- Default settings/parameters for "CGLipidBr2005" -- - # (Hybrid bond & angle styles were used for portability.) - - # As in Watson(JCP 2011), rigid bond-length constraints - # have been replaced by harmonic bonds. - # The k_theta parameter should lie in between 5*epsilon and 10*epsilon. - bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2 - } - - write_once("In Settings") { - # cosine/delta: U(theta) = k*(1-cos(theta-theta0)) - #angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps - # harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2 - angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps - } - # I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper - # to attempt to compensate for the fact that here we are using a lipid - # mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal - # of disorder into the bilayer which would not be present in a DPPC bilayer. - # This causes pores to form. Increasing the angle stiffness prevents this.) - - write_once("In Settings") { - - # The interaction of "atom:int" with other "atom:int" atoms is given by - # epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at - # r=3*sigma. This was implemented using pair_style table. - # Unfortunately, mixing lj/charmm and "table" pair styles in the same - # simulation is very inneficient. - - pair_coeff @atom:int @atom:int table table_int.dat INT - - # The interaction of tail beads with eachother is given by the formula below - # and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules: - # epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6), - pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # The interaction of head beads which all other beads is given by: - # epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6), - - pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - } # write_once("In Settings") - - # Note: I divided epsilon by 4 to get "0.1643" because we are using the - # "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6) - # (The "es4k4l" coeffstyle is the default.) Using this convention makes it - # easier to mix this coarse-grained lipid model with other molecular models. - - - -} # CGLipidBr2005 - - - - - - - - -# Note: This example has not been optimized for speed. -# -# Unfortunately, using both lj/charmm and "table" pair styles in the same -# simulation seems to be very inneficient. (The simulation is twice as slow -# as using only the "lj/charmm" pair styles for every pairwise interaction, -# ...and about 25% slower than using "table" for every pairwise interaction. -# However the lennard-jones pair styles support mixing, so we use them to -# make it easier to run these molecules with other molecules which don't use -# pair_table. I felt that portability was worth the extra 25% slow down.) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh deleted file mode 100755 index b0de637379..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/README.sh +++ /dev/null @@ -1,22 +0,0 @@ -# This example shows how to build a multicomponent spherical vesicle. -# The lipid bilayer is composed of two different lipids (DPPC and DLPC), -# The vesicle contains 120 trans-membrane protein inclusions. -# -# ---------------- Prerequisites: ------------------ -# You must run packmol to generate the coordinates beforehand. -# Afterwards, move and rename the final coordinate file to "../system.xyz" -# To do this, check the README.sh file in the ../packmol_files directory. -# (or follow these instructions below) -# -# cd ../packmol_files -# packmol < step1_proteins.inp -# packmol < step2_innerlayer.inp -# packmol < step3_outerlayer.inp -# cp step3_outerlayer.xyz ../system.xyz -# -# These steps could take a few hours. -# -# --- After you have done that, you can run moltemplate using this command: --- - -moltemplate.sh system.lt -xyz ../system.xyz - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py deleted file mode 100755 index 1eb97e6454..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py +++ /dev/null @@ -1,34 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity) - -# The previous version included the repulsive core term -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) -# We don't want to do that. Instead compute the core repulsion using a -# different pair_style and add the attractive term on top of it using the table. -# This way it the core repulsion acts as a default interaction with other atom -# types (using the new repulsive mixing rules). - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -rcut = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma) - F_r = F(r, epsilon, sigma) - if r > rcut: - U_r = 0.0 - F_r = 0.0 - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index 32147e444a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python - -# Calculate a table of pairwise energies and forces between "INT" atoms -# in the lipid membrane model described in -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) -# I realized later this is not what we want because although energy is conserved -# all enrgies are shifted with respect to energies used in the Brannigan paper -# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole). -# (So don't use this.) - -# Calculate and print a - -def S(r, rc1, rc2, derivative=False): - """ - Calculate the switching function S(r) which decays continuously - between 1 and 0 in the range from rc1 to rc2 (rc2>rc1): - S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 - I'm using the same smoothing/switching cutoff function used by the CHARMM - force-fields. (I'm even using the same code to implement it, taken - from lammps charmm/coul/charmm pair style, rewritten in python.) - - """ - assert(rc2>rc1) - rsq = r*r - rc1sq = rc1*rc1 - rc2sq = rc2*rc2 - denom_lj_inv = (1.0 / ((rc2sq-rc1sq)* - (rc2sq-rc1sq)* - (rc2sq-rc1sq))) - if rsq > rc2sq: - return 0.0 - elif rsq < rc1sq: - if derivative: - return 0.0 - else: - return 1.0 - else: - rc2sq_minus_rsq = (rc2sq - rsq) - rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq - if derivative: - return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv) - else: - return (rc2sq_minus_rsq_sq * - (rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv) - - -def U(r, eps, sigma): - return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r)) - -def F(r, eps, sigma): - return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r)) - -epsilon = 2.75/4.184 # kCal/mole -sigma = 7.5 -Rmin = 0.02 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1130 - -for i in range(0,N): - r = Rmin + i*(Rmax-Rmin)/(N-1) - U_r = U(r, epsilon, sigma) - F_r = F(r, epsilon, sigma) - # Multiply U(r) & F(r) by the smoothing/switch function - U_r = U_r * S(r, Rc1, Rc2) - F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False) - print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r)) - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt deleted file mode 100644 index 98213116d8..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt +++ /dev/null @@ -1,192 +0,0 @@ -# Description: -# -# This example shows how to build a multicomponent spherical vesicle. -# The lipid bilayer is composed of two different lipids (DPPC and DLPC), -# The vesicle contains 120 trans-membrane protein inclusions. -# -# The DPPC lipid model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The protein model is described here: -# G. Bellesia, AI Jewett, and J-E Shea, -# Protein Science, Vol19 141-154 (2010) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to -# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293 -# -# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below) -# -# NOTE: -# This example may require additional features to be added to LAMMPS. -# If LAMMPS complains about an "Invalid pair_style", then copy the code -# in the "additional_lammps_code" directory into your LAMMPS "src" directory -# and recompile LAMMPS. - -# First, load the definitions of the molecules we will need: - -import "CGLipidBr2005.lt" -using namespace CGLipidBr2005 - -import "1beadProtSci2010.lt" -using namespace 1beadProtSci2010 - -# PREREQUISITES: -# Coordinates for the molecules in this example are loaded from an .XYZ file -# created by PACKMOL. This must be done in advance. (See ../packmol_files/) -# -# The XYZ file was created by PACKMOL in 3 steps: -# (Add the proteins, then pack lipids in the inner & outer layers around them.) -# -# step1) Creae 120 proteins. Distribute them on the surface of the sphere. -# -# step2) Keeping the coordinates from step1 fixed, -# a) first we add 9500 DPPC lipids to the inner monolayer -# b) then we add 9500 DLPC lipids to the inner monolayer -# -# step3) Keeping the coordinates from steps 1 and 2 fixed, -# a) first we add 12500 DPPC lipids to the outer monolayer -# b) then we add 12500 DLPC lipids to the outer monolayer -# -# The order that molecules are created in moltemplate should match the order -# they appear in the final XYZ file created by PACKMOL. (See above.) -# Consequently I instantiate the molecules in the same order here: - - -# Step 1) ---- protein inclusions ---- - -proteins = new 4HelixInsideOut [120] - -# Step 2a) ---- inner monolayer ---- -dppc_in = new DPPC [9500] -# Step 2b) -dlpc_in = new DLPC [9500] - -# Step 3a) ---- outer monolayer ---- -dppc_out = new DPPC [12500] -# Step 3b) -dlpc_out = new DLPC [12500] - - - -# ------------------ boundary conditions -------------------- - -write_once("Data Boundary") { - -500.0 500.0 xlo xhi - -500.0 500.0 ylo yhi - -500.0 500.0 zlo zhi -} - - -write_once("In Settings") { - - # ----------------------------------------------------------- - # -------- interactions between protein and lipids ---------- - # ----------------------------------------------------------- - - # Interactions between the protein and lipid atoms are usually - # determined by mixing rules. (However this is not possible some - # for atoms, such as the "int" atoms in the lipid model which - # interact using -1/r^2 attraction.) Mixing rules do not make - # sense for these atoms so we must explicitly define their - # interaction with all other atoms. - - # We want the hydrophobic interactions between hydrophobic residues in - # the protein and beads the interior of the lipid to be energetically - # similar to the attractive interactions between the lipid tails. - # - # Note: I made the width of the outward-facing protein beads slightly larger - # ("12.5") whenever they interact with the "tail" beads in each lipid - # (in order to make the protein wider there). - # This hopefully relieves some of the internal negative pressure in the center - # of the bilayer which can otherwise rip apart the protein or suck it into - # the bilaer. (This is a hack, and I'm not sure if it is necessary. - # For different protein or lipid models, you probably don't need this.) - # - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1 - - # To help keep the protein from tilting 90 degrees and burying itself - # within the lipid bilayer, we make the turn regions at either - # end of the protein (strongly) attracted to the head groups - # of the lipid. (In reality, they would probably be attracted - # to the water as well.) - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # All other interactions between proteins and lipids are steric. - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - - - # ----------------------------------------------------------- - # -------- Modifications to the protein model: -------------- - # ----------------------------------------------------------- - # - # Turn off attraction between the hydrophobic "@atom:sH" beads: - # (These beads are located in the outside of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0 - - # (Why: These beads are only attracted to - # each other in an aqueous environment) - - # ... and - # Turn ON attraction between the hydrophilic "@atom:sL" beads. - # (These beads are located in the interior of a trans-membrane protein.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1 - - # Why? - # In reality, polar groups in the interior of trans-membrane - # proteins do form hydrogen bonds with each other. This was - # absent from the original protein model because, in an aqueous - # environment, these groups preferentially interact with the water. - # - # Why is this necessary? - # Shouldn't attraction between lipid tails and the protein create - # an effective force which brings the hydrophilic beads together? - # (similar to the hydrophobic effect, but in reverse?). - # Answer: - # Unlike an aqueous environment (~zero pressure, or +1atm), there is - # a large negative pressure in the interior of some bilayer membrane - # models (such as this one). Without some kind of direct attraction - # between interior residues, the protein will get pulled apart. - # (Perhaps the attractive force I am using is too strong?) - -} - - -# Finally, we must combine the two force-field styles which were used for -# the coarse-grained lipid and protein. To do that, we write one last time -# to the "In Init" section. When reading the "Init" section LAMMPS will -# read these commands last and this will override any earlier settings. - -write_once("In Init") { - # -- These styles override earlier settings -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid cosine/delta harmonic - dihedral_style hybrid fourier - improper_style none - pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - communicate multi -} - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat deleted file mode 100644 index b0d651d67f..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1139 +0,0 @@ -# Table for the INT-INT interaction from -# Brannigan et al, Phys Rev E, 72, 011915 (2005) -# This table contains -# i r_i U(r_i) -dU/dr|r_i -# where U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2) - -INT -N 1130 - -1 0.02 2.0331818401e+30 1.21990910406e+33 -2 0.04 4.9638228518e+26 1.48914685554e+29 -3 0.06 3.82579033251e+24 7.65158066501e+26 -4 0.08 1.21187081343e+23 1.81780622014e+25 -5 0.1 8.32791281704e+21 9.99349538045e+23 -6 0.12 9.34030842897e+20 9.34030842897e+22 -7 0.14 1.46892540453e+20 1.25907891817e+22 -8 0.16 2.95866897809e+19 2.21900173357e+21 -9 0.18 7.19889946863e+18 4.79926631242e+20 -10 0.2 2.0331818401e+18 1.21990910406e+20 -11 0.22 6.47834392264e+17 3.53364213962e+19 -12 0.24 2.28034873754e+17 1.14017436877e+19 -13 0.26 8.72681951932e+16 4.02776285507e+18 -14 0.28 3.58624366341e+16 1.53696157003e+18 -15 0.3 1.56704372019e+16 6.26817488078e+17 -16 0.32 7.2233129348e+15 2.70874235055e+17 -17 0.34 3.48970861422e+15 1.23166186384e+17 -18 0.36 1.75754381558e+15 5.85847938527e+16 -19 0.38 9.18613895646e+14 2.90088598625e+16 -20 0.4 4.96382285179e+14 1.48914685554e+16 -21 0.42 2.76404230108e+14 7.89726371739e+15 -22 0.44 1.58162693423e+14 4.31352800247e+15 -23 0.46 9.27773983256e+13 2.42027995633e+15 -24 0.48 5.56725765996e+13 1.391814415e+15 -25 0.5 3.41111308981e+13 8.18667141564e+14 -26 0.52 2.13057117167e+13 4.91670270393e+14 -27 0.54 1.35459994024e+13 3.0102220895e+14 -28 0.56 8.75547769351e+12 1.87617379153e+14 -29 0.58 5.74645813711e+12 1.18892237325e+14 -30 0.6 3.8257903322e+12 7.65158066491e+13 -31 0.62 2.58128463312e+12 4.99603477424e+13 -32 0.64 1.7635041342e+12 3.30657025205e+13 -33 0.66 1.21901470178e+12 2.21639036726e+13 -34 0.68 8.51979641904e+11 1.50349348607e+13 -35 0.7 6.0167184547e+11 1.0314374497e+13 -36 0.72 4.29087845387e+11 7.15146409276e+12 -37 0.74 3.08855637556e+11 5.00846980094e+12 -38 0.76 2.24270970425e+11 3.54112058818e+12 -39 0.78 1.64210505205e+11 2.52631546702e+12 -40 0.8 1.2118708117e+11 1.81780621971e+12 -41 0.82 90109367359.1 1.31867367068e+12 -42 0.84 67481501334.4 9.64021449503e+11 -43 0.86 50880896383.4 7.09965997788e+11 -44 0.88 38613938681.2 5.26553710913e+11 -45 0.9 29486692086.8 3.93155896009e+11 -46 0.92 22650731882.4 2.95444330322e+11 -47 0.94 17498544395.3 2.23385674464e+11 -48 0.96 13591937526.4 1.69899220331e+11 -49 0.98 10612635712.6 1.29950642555e+11 -50 1.0 8327912706.34 99934953582.6 -51 1.02 6566502316.69 77252969474.2 -52 1.04 5201589672.36 60018343356.8 -53 1.06 4138717434.11 46853405843.3 -54 1.08 3307128665.58 36745874940.0 -55 1.1 2653529579.27 28947596241.1 -56 1.12 2137567708.15 22902511945.9 -57 1.14 1728534024.3 18195095739.0 -58 1.16 1402943799.0 14513212422.1 -59 1.18 1142752163.37 11621209113.9 -60 1.2 934030766.093 9340308300.6 -61 1.22 765981286.774 7534242773.65 -62 1.24 630196371.787 6098675145.29 -63 1.26 520103253.414 4953364870.6 -64 1.28 430542934.103 4036340534.04 -65 1.3 357450462.101 3299543229.91 -66 1.32 297610947.802 2705554551.18 -67 1.34 248472587.186 2225128105.44 -68 1.36 208002782.573 1835319108.76 -69 1.38 174576985.011 1518061159.35 -70 1.4 146892484.084 1259078837.33 -71 1.42 123901294.937 1047053582.16 -72 1.44 104757721.536 872981382.419 -73 1.46 88777241.639 729676313.267 -74 1.48 75404158.02 611385405.387 -75 1.5 64186061.7033 513488820.507 -76 1.52 54753607.1486 432265633.695 -77 1.54 46804443.7318 364710253.134 -78 1.56 40090410.0598 308388060.159 -79 1.58 34407297.9713 261321529.95 -80 1.6 29586646.6744 221900119.2 -81 1.62 25489145.661 188808745.634 -82 1.64 21999316.2868 160970856.824 -83 1.66 19021212.5921 137502982.517 -84 1.68 16474936.8715 117678352.86 -85 1.7 14293808.3245 100897694.735 -86 1.72 12422056.6082 86665727.6626 -87 1.74 10812938.3788 74572197.8496 -88 1.76 9427195.57103 64276535.39 -89 1.78 8231790.46096 55495411.7777 -90 1.8 7198865.45512 47992625.088 -91 1.82 6304885.77339 41570857.9644 -92 1.84 5529931.32911 36064946.1544 -93 1.86 4857110.59557 31336368.341 -94 1.88 4272074.43377 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30.000000 - 2 0.000000 0.000000 22.500000 - 3 0.000000 0.000000 15.000000 - 3 0.000000 0.000000 7.500000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz deleted file mode 100644 index c25a2dbd1a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/DPPC.xyz +++ /dev/null @@ -1,7 +0,0 @@ -5 - DPPC coarse-grained lipid - 1 0.000000 0.000000 33.750000 - 2 0.000000 0.000000 26.250000 - 3 0.000000 0.000000 18.750000 - 3 0.000000 0.000000 11.250000 - 3 0.000000 0.000000 3.750000 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh deleted file mode 100644 index daf17fa827..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/README.sh +++ /dev/null @@ -1,20 +0,0 @@ -# Here we generate the starting coordinates of the simulation -# using PACKMOL - -# You must run each packmol commend one after the other -# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding -# "inp" file. This should not happen. You can also usually interrupt -# packmol after 30 minutes, and the solution at that point should be good -# enough for use. -packmol < step1_proteins.inp # This step determines the protein's location - # It takes ~20 minutes (on an intel i7) -packmol < step2_innerlayer.inp # this step builds the inner monolayer - # It takes ~90 minutes -packmol < step3_outerlayer.inp # this step builds the outer monolayer - # It takes ~4 hours - -# Running these three commands will probably take about an hour. -# (It depends on how uniformly you need the packing to be.) - -mv -f step3_outerlayer.xyz ../system.xyz - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz deleted file mode 100644 index 75557e6ffb..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/protein.xyz +++ /dev/null @@ -1,75 +0,0 @@ -73 - -6 -2.11383 -5.225 -29.7 -6 -5.225 -2.11383 -26.4 -7 -8.33617 -5.225 -23.1 -7 -5.225 -8.33617 -19.8 -6 -2.11383 -5.225 -16.5 -6 -5.225 -2.11383 -13.2 -7 -8.33617 -5.225 -9.9 -7 -5.225 -8.33617 -6.6 -6 -2.11383 -5.225 -3.3 -6 -5.225 -2.11383 0 -7 -8.33617 -5.225 3.3 -7 -5.225 -8.33617 6.6 -6 -2.11383 -5.225 9.9 -6 -5.225 -2.11383 13.2 -7 -8.33617 -5.225 16.5 -7 -5.225 -8.33617 19.8 -6 5.225 -2.11383 -26.4 -6 2.11383 -5.225 -23.1 -7 5.225 -8.33617 -19.8 -7 8.33617 -5.225 -16.5 -6 5.225 -2.11383 -13.2 -6 2.11383 -5.225 -9.9 -7 5.225 -8.33617 -6.6 -7 8.33617 -5.225 -3.3 -6 5.225 -2.11383 0 -6 2.11383 -5.225 3.3 -7 5.225 -8.33617 6.6 -7 8.33617 -5.225 9.9 -6 5.225 -2.11383 13.2 -6 2.11383 -5.225 16.5 -7 5.225 -8.33617 19.8 -7 8.33617 -5.225 23.1 -6 2.11383 5.225 -23.1 -6 5.225 2.11383 -19.8 -7 8.33617 5.225 -16.5 -7 5.225 8.33617 -13.2 -6 2.11383 5.225 -9.9 -6 5.225 2.11383 -6.6 -7 8.33617 5.225 -3.3 -7 5.225 8.33617 0 -6 2.11383 5.225 3.3 -6 5.225 2.11383 6.6 -7 8.33617 5.225 9.9 -7 5.225 8.33617 13.2 -6 2.11383 5.225 16.5 -6 5.225 2.11383 19.8 -7 8.33617 5.225 23.1 -7 5.225 8.33617 26.4 -6 -5.225 2.11383 -19.8 -6 -2.11383 5.225 -16.5 -7 -5.225 8.33617 -13.2 -7 -8.33617 5.225 -9.9 -6 -5.225 2.11383 -6.6 -6 -2.11383 5.225 -3.3 -7 -5.225 8.33617 0 -7 -8.33617 5.225 3.3 -6 -5.225 2.11383 6.6 -6 -2.11383 5.225 9.9 -7 -5.225 8.33617 13.2 -7 -8.33617 5.225 16.5 -6 -5.225 2.11383 19.8 -6 -2.11383 5.225 23.1 -7 -5.225 8.33617 26.4 -7 -8.33617 5.225 29.7 -8 -3.35683 -4.56775 24.0698 -8 0.795667 -6.90708 26.8152 -8 4.78683 -3.13225 27.0802 -8 2.75642 6.08575 -28.7448 -8 6.54133 3.72717 -31.9651 -8 5.58525 -1.68575 -31.7552 -8 3.35683 4.56775 29.8448 -8 -0.795667 6.90708 32.5903 -8 -4.78683 3.13225 32.8552 diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp deleted file mode 100644 index abb48db7d6..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step1_proteins.inp +++ /dev/null @@ -1,49 +0,0 @@ -# Step 1: Create a sphere of proteins lying -# (In step 2 we will pack lipids around these proteins -# -# ----- Run using: ----- -# packmol < step1_proteins.inp -# (This takes about 30 minutes on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent proteins will be at least 50.0 Angstrons apart. -tolerance 50.0 -# (Setting "discale" to 2.0 increases the typical separation -# distance to approximately 2.0*50.0 = 100.0 Angstroms.) -discale 2.0 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step1_proteins.xyz - - -# File types are in xyz format - -filetype xyz - - - -# First, specify the protein inclusions -# We will pack the lipids around these later - -structure protein.xyz - number 120 - atoms 68 69 70 - inside sphere 0. 0. 0. 273.75 - end atoms - atoms 65 66 67 71 72 73 - outside sphere 0. 0. 0. 325.0 - end atoms -end structure - - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp deleted file mode 100644 index 9f61960f2e..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step2_innerlayer.inp +++ /dev/null @@ -1,70 +0,0 @@ -# NOTE: YOU MUST COMPLETE STEP 1 BEFORE RUNNING PACKMOL ON THIS FILE - -# Step 2: Pack the lipids in the inner monolayer around the proteins from step1. -# -# ----- Run using: ----- -# packmol < step2_innerlayer.inp -# (This takes about 90 minutes on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent molecules will be at least 5.5 Angstrons apart -tolerance 5.5 -# (Setting "discale" to 1.4 increases the typical separation -# distance to approximately 1.4*5.5 = 7.7 Angstroms.) -discale 1.4 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step2_innerlayer.xyz - -# File types are in xyz format - -filetype xyz - - -# The proteins whose position we determined earlier in step 1 -# will be frozen in place during this step. - -structure step1_proteins.xyz - number 1 - fixed 0. 0. 0. 0. 0. 0. -end structure - - -# 9500 DPPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing inwards, and their tails (atom 5) pointing outwards. - - -structure DPPC.xyz - number 9500 - atoms 1 - inside sphere 0. 0. 0. 270.0 - end atoms - atoms 5 - outside sphere 0. 0. 0. 295.0 - end atoms -end structure - -# 9500 DLPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing inwards, and their tails (atom 4) pointing outwards. - -structure DLPC.xyz - number 9500 - atoms 1 - inside sphere 0. 0. 0. 273.0 - end atoms - atoms 4 - outside sphere 0. 0. 0. 295.0 - end atoms -end structure - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp deleted file mode 100644 index bed1c04246..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/packmol_files/step3_outerlayer.inp +++ /dev/null @@ -1,70 +0,0 @@ -# NOTE: YOU MUST COMPLETE STEPS 1 AND 2 BEFORE RUNNING PACKMOL ON THIS FILE - -# Step 3: Pack the lipids in the outer monolayer around the proteins from step1. -# -# ----- Run using: ----- -# packmol < step3_outerlayer.inp -# (This takes about 4 hours on an Intel i7 processor) - - -# ----- Settings: ----- - -# All the atoms from diferent molecules will be at least 5.5 Angstrons apart -tolerance 5.5 -# (Setting "discale" to 1.4 increases the typical separation -# distance to approximately 1.4*5.5 = 7.7 Angstroms.) -discale 1.4 -# The other parameters below are optional: -nloop 10000 -maxit 20 -seed 12345 -sidemax 3000.0 -# What fraction of the molecules are moved during "large moves"? (default 0.05) -movefrac 0.05 - - -# The output file name - -output step3_outerlayer.xyz - -# File types are in xyz format - -filetype xyz - - -# The proteins and lipids whose position we determined earlier in steps 1-2 -# will be frozen in place during this step. - -structure step2_innerlayer.xyz - number 1 - fixed 0. 0. 0. 0. 0. 0. -end structure - - -# 12500 DPPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing outwards, and their tails (atom 5) pointing inwards. - - -structure DPPC.xyz - number 12500 - atoms 5 - inside sphere 0. 0. 0. 310.0 - end atoms - atoms 1 - outside sphere 0. 0. 0. 336.0 - end atoms -end structure - -# 12500 DLPC lipids will be put in a shell with their hydrophilic heads -# (atom 1) pointing outwards, and their tails (atom 4) pointing inwards. - -structure DLPC.xyz - number 12500 - atoms 4 - inside sphere 0. 0. 0. 313.0 - end atoms - atoms 1 - outside sphere 0. 0. 0. 332.0 - end atoms -end structure - diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min deleted file mode 100644 index cb374fea13..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.min +++ /dev/null @@ -1,58 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. - - - -# -- Init section -- - -include system.in.init - -# -- Atom definition section -- - -read_data system.data - -# Read in the coordinates generated by packmol: -# (This takes a while, unfortunately.) - -include system.in.coords - -# If you repeat minimization later, you can skip the (slow) step above which -# reads the coordinaes, by commenting it out and uncommenting this line below: -# -# read_restart system_t0.rst - -# -- Settings Section -- - -include system.in.settings - -# -- Run section -- - -write_restart system_t0.rst - -dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz - -# minimize - -minimize 1.0e-5 1.0e-7 5000 20000 - -# If minimization crashes, then instead try Langevin dynamics -# with a small timestep and a fast damping parameter. For example: -# -# timestep 0.05 -# fix fxlan all langevin 300.0 300.0 100.0 48279 -# fix fxnve all nve -# -# run 10000 - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt deleted file mode 100644 index 3cb0e7067a..0000000000 --- a/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/run.in.nvt +++ /dev/null @@ -1,70 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC") -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -# 2) It also may require additional features and bug fixes for LAMMPS. -# So, after typing "make yes-user-misc" in to the shell, ... -# be sure to download and copy the "additional_lammps_code" from -# http://moltemplate.org (upper-left corner menu) -# 3) Unpack it -# 4) copy the .cpp and .h files to the src folding of your lammps installation. -# 5) Compile LAMMPS. -# -# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style" -# then you made a mistake in the instructions above. -# -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# Commenting out: -# -# read_data system.data -# -# Instead read the restart file created by "run.in.min". - -read_restart system_after_min.rst - -# WARNING: Unfortunately the LAMMPS "read_restart" command has been undependable -# over the past year (2012). If this fails, then just move the minimization -# steps in run.in.min into this script (into the "Run Section"). -# Alternately, try to extract the last frame of the dump file created -# by run.in.min using "read_dump", "dump2data.py", and/or "restart2data". - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -# Just in case the previous minimization failed, try again. -# (I don't know why this would help, but sometimes loading -# up the restart file and trying again does help. Magic.) - -minimize 1.0e-5 1.0e-7 5000 20000 - -# Run main simulation - -timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs -dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz - - -thermo_style custom step temp pe etotal vol epair ebond eangle -thermo 100 # time interval for printing out "thermo" data - - - - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB. -# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon. -# Note: The langevin damping parameter "120" corresponds to -# the 0.12ps damping time used in Watson et. al JCP 2011. - -run 1000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT deleted file mode 100644 index c3173a1e19..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README.TXT +++ /dev/null @@ -1,17 +0,0 @@ - -This directory contains an example of a couarse-grained (vaguely protein-like) -heteropolymer consisting of 14 residues, each of which has 2 atoms -(one backbone atom, one residue atom.) - -There are two types of residues, H and P. -The R-atom for the H residue are attracted to eachother. -All other atoms are repulsive. - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh deleted file mode 100755 index 1347aebbb4..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh +++ /dev/null @@ -1,20 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.nvt - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt deleted file mode 100644 index 5d97ea56ad..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualize.txt +++ /dev/null @@ -1,86 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg deleted file mode 100644 index a57d0309c3..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg deleted file mode 100644 index c77d7ee9d9..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/2bead_heteropolymer_t=1000ps.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index a30fdf733f..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,1728 +0,0 @@ -PSF - 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730 729 731 732 742 741 743 744 - 744 743 745 746 754 753 755 756 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 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This means that whenever -# an atom type (or other counter variable) appears inside a molecule -# definition using the normal syntax "@atom:R", that atom type is a local -# property of the the "H" or "P" molecule in which it appears. -# Any properties assigned to the "R" atoms in either molecule are unique -# to that molecule. -# -# However in order to share "CA" atom types, we will override this behavior -# using the "@atom:../CA" syntax instead of "@atom:CA". This will define -# the "CA" atom in the outer (global) environment, and any properties -# (mass, radius, etc...) assigned to the "@atom:../CA" atom apply to -# "CA" atoms in both the the "H" and "P" molecules (and everywhere else). -# -# This might not be a desirable. "CA" is a popular name for carbon -# atoms in different types of molecules. We don't want to prevent other -# molecules from using this atom name. So we enclose the "CA" atom, -# (along with the definitions of the "H" and "P" molecules) within a -# namespace/environment object ("2bead"). This makes the definition -# of "H" and "P" more portable. Later on we can combine "H" and "P" -# molecules with other molecules without worrying whether they contain -# "CA" atoms with different properties. -# -# Note: In this example "2bead" is NOT a molecule. (Because it contains no -# "write("Data Atoms")" section of its own.) "2bead" is simply the -# name of an environment in which other molecules (H,P) are defined. - - - - -2bead { - - # LAMMPS supports a large number of force-field styles. We must select - # which ones we need. This information belongs in the "In Init" section. - # (Hybrid styles used for portability. These choices can be overridden later.) - - write_once("In Init") { - # -- Default styles for "2bead" -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid charmm - pair_style hybrid lj/cut 11.0 - - # If charges are needed, (assuming biopolymers), try one of: - #dielectric 80.0 - #pair_style hybrid lj/cut/coul/debye 0.1 11.0 - # or (for short distances, below a couple nm) - #pair_style hybrid lj/charmm/coul/charmm/implicit 9.0 11.0 - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - - # Define H (the "hydrophobic" residue) - H { - # atom-id mol-id atom-type charge x y z - write("Data Atoms") { - $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 - $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 - } - write("Data Bonds") { - $bond:CR @bond:../sidechain $atom:CA $atom:R - } - } - - - # Define P (the "polar" residue) - P { - # atom-id mol-id atom-type charge x y z - write("Data Atoms") { - $atom:CA $mol:... @atom:../CA 0.0 0.000 1.0000 0.0000000 - $atom:R $mol:... @atom:R 0.0 0.000 4.4000 0.0000000 - } - write("Data Bonds") { - $bond:CR @bond:../sidechain $atom:CA $atom:R - } - } - - # (Note: Again, atom types, bond-types, (dihedral-types, any variable, etc) - # can be shared. The ".." in "@atom:../CA" tells moltemplate that - # atom type CA is defined in the parent's environment. (We are - # sharing the CA atom type between both the H and P residues. - # The same is true of the ".." in "@bond:../sidechain". - # - # - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # molecule's id number as it's own. - - - - # There are 3 atom types: the R sidechain (belonging to the H and P residues) - # and the CA sidechain atom (shared by both residues) - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:H/R 50.0 - @atom:P/R 50.0 - } - - - # -------------------------------------------------------------------- - # -- In this example, all force field parameters are stored in the -- - # -- file named "In Settings". They can also go in sections like -- - # -- "Data Pair Coeffs", "Data Bond Coeffs", "Data Angle Coeffs"... -- - # -------------------------------------------------------------------- - - - # 2-body (non-bonded) interactions: - # - # Uij(r) = 4*eps_ij * ( (sig_ij/r)^12 - (sig_ij/r)^6 ) - # - # Hydrophobic side-chains are attractive (large epsilon parameter). - # Polar side-chains and backbone atoms are not attractive (small epsilon). - # - # i j pairstylename eps sig - # - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA lj/cut 0.10 2.0 - pair_coeff @atom:H/R @atom:H/R lj/cut 2.50 3.6 - pair_coeff @atom:P/R @atom:P/R lj/cut 0.10 3.6 - } - # - # (Interactions between different atom types use "arithmetic" mixing rules.) - - - # 2-body (bonded) interactions: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType bondstylename k r0 - # - - write_once("In Settings") { - bond_coeff @bond:sidechain harmonic 30.0 3.4 - bond_coeff @bond:backbone harmonic 30.0 3.7 - } - -} # 2bead - diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt deleted file mode 100644 index c378609ac3..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/2bead_angles.lt +++ /dev/null @@ -1,61 +0,0 @@ -# Although there's no need to define angular interactions (because the "H" -# and "P" molecules only contains two atoms), we define the settings for angles -# or dihedrals which might be present later when we connect multiple "H" and "P" -# molecules together to build a polymer. - -2bead { - - # OPTIONAL: Enclose these angle settings within the 2bead {...} environment. - # We do this for the same reason we enclosed "H" and "P" in "2bead". - # This does not overwrite the definition of 2bead. Here we are only - # augmenting "2bead" to include definitions of the following angles - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:*/R @bond:* @bond:* - } - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - @dihedral:RCCR @atom:*/R @atom:CA @atom:CA @atom:*/R @bond:* @bond:* @bond:* - } - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # (k in kcal/mol/rad^2, theta0 in degrees) - # - # The corresponding command is: - # - # angle_coeff angleType anglestylename k theta0 - - write_once("In Settings") { - angle_coeff @angle:backbone harmonic 30.00 114 - angle_coeff @angle:sidechain harmonic 30.00 123 - } - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # - # The corresponding command is - # dihedral_coeff dihedralType dihedralstylename K n d w - # "w" is the weight for 1-4 pair interactions, which we set to 0.0 - - write_once("In Settings") { - dihedral_coeff @dihedral:CCCC charmm -0.5 1 -180 0.0 - dihedral_coeff @dihedral:RCCR charmm -1.5 1 -180 0.0 - } # write_once("In Settings") - -} \ No newline at end of file diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh deleted file mode 100755 index 7604a672c6..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/README.sh +++ /dev/null @@ -1,20 +0,0 @@ -# The version of "2bead.lt" in this directory is defines two types of -# molecules (named "2bead/H" and "2bead/P"). -# -# However, there is another version of this file which is easier to understand. -# I recommend reading that file first. -# It is located at "simplified_version_one_residue/2bead.lt". -# It defines only one type of molecule (named "2bead") -# It is much simpler. - -# ------ - -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - -# run moltemplate - -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data. - diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt deleted file mode 100644 index 6c70892444..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/peptide.lt +++ /dev/null @@ -1,51 +0,0 @@ -import "2bead.lt" -import "2bead_angles.lt" - -Peptide { - - # A polymer of alternating "H" and "P" beads: - - res1 = new 2bead/P - res2 = new 2bead/P.rot(180.0, 1,0,0).move(3.2,0,0) - res3 = new 2bead/H.rot( 0.0, 1,0,0).move(6.4,0,0) - res4 = new 2bead/H.rot(180.0, 1,0,0).move(9.6,0,0) - res5 = new 2bead/H.rot( 0.0, 1,0,0).move(12.8,0,0) - res6 = new 2bead/H.rot(180.0, 1,0,0).move(16.0,0,0) - res7 = new 2bead/P.rot( 0.0, 1,0,0).move(19.2,0,0) - res8 = new 2bead/P.rot(180.0, 1,0,0).move(22.4,0,0) - res9 = new 2bead/P.rot( 0.0, 1,0,0).move(25.6,0,0) - res10 = new 2bead/H.rot(180.0, 1,0,0).move(28.8,0,0) - res11 = new 2bead/H.rot( 0.0, 1,0,0).move(32.0,0,0) - res12 = new 2bead/H.rot(180.0, 1,0,0).move(35.2,0,0) - res13 = new 2bead/P.rot( 0.0, 1,0,0).move(38.4,0,0) - res14 = new 2bead/P.rot(180.0, 1,0,0).move(41.6,0,0) - - # Now, link the residues together this way: - write("Data Bonds") { - $bond:backbone1 @bond:2bead/backbone $atom:res1/CA $atom:res2/CA - $bond:backbone2 @bond:2bead/backbone $atom:res2/CA $atom:res3/CA - $bond:backbone3 @bond:2bead/backbone $atom:res3/CA $atom:res4/CA - $bond:backbone4 @bond:2bead/backbone $atom:res4/CA $atom:res5/CA - $bond:backbone5 @bond:2bead/backbone $atom:res5/CA $atom:res6/CA - $bond:backbone6 @bond:2bead/backbone $atom:res6/CA $atom:res7/CA - $bond:backbone7 @bond:2bead/backbone $atom:res7/CA $atom:res8/CA - $bond:backbone8 @bond:2bead/backbone $atom:res8/CA $atom:res9/CA - $bond:backbone9 @bond:2bead/backbone $atom:res9/CA $atom:res10/CA - $bond:backbone10 @bond:2bead/backbone $atom:res10/CA $atom:res11/CA - $bond:backbone11 @bond:2bead/backbone $atom:res11/CA $atom:res12/CA - $bond:backbone12 @bond:2bead/backbone $atom:res12/CA $atom:res13/CA - $bond:backbone13 @bond:2bead/backbone $atom:res13/CA $atom:res14/CA - } - - create_var { $mol } # <--create a molecule ID number for this peptide - - # This causes res1,res2,res3,...,res14 to share the same molecule counter - # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks - # for a counter of that type in a parent molecule or earlier ancestor. - -} # Peptide - - - -# Angle, dihedral and improper interactions will be generated -# according to the instructions in "2bead_angles.lt" diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt deleted file mode 100644 index eea38da04a..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/simplified_version_one_residue/2bead_simple.lt +++ /dev/null @@ -1,122 +0,0 @@ -# This file contains the definition of "2-bead", a simple molecule -# containing two atoms: -# -# @R -# | -# @CA -# -# -# Later on, we may connect them together to form a polymer: -# -# -# @R @R -# | | -# _@CA_ _@CA_ -# ... -.@CA-' `-@CA-' ` ... -# | | -# @R @R -# -# THERE ARE TWO VERSIONS OF THIS FILE: -# In the simple version, shown here, there is only one type of side-chain "R". -# More complex examples have multiple types of molecules -# each with different side-chain properties. - -2bead { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA 0.0 0.000 0.0000 0.0000000 - $atom:R $mol:... @atom:R 0.0 0.000 3.4000 0.0000000 - } - - write_once("Data Masses") { - @atom:C 14.0 - @atom:R 50.0 - } - - write("Data Bonds") { - $bond:CR @bond:sidechain $atom:CA $atom:R - } - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - } - - write_once("Data Dihedrals By Type") { - @dihedral:CCCC @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - @dihedral:RCCR @atom:R @atom:CA @atom:CA @atom:R @bond:* @bond:* @bond:* - } - - - write_once("In Settings") { - # 2-body (bonded) interaction parameters are listed by bondType: - # - # Ubond(r) = (k/2)*(r-0)^2 - # - # The corresponding command is: - # - # bond_coeff bondType harmonic k r0 - # - bond_coeff @bond:sidechain harmonic 30.0 3.4 - bond_coeff @bond:backbone harmonic 30.0 3.7 - - # 3-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Uangle(theta) = (k/2)*(theta-theta0)^2 - # - # The corresponding command is: - # - # angle_coeff angleType harmonic k theta0 - # (The theta0 parameter is in degrees, k is in kcal/mol/rad^2) - - angle_coeff @angle:backbone harmonic 30.0 104 - angle_coeff @angle:sidechain harmonic 30.0 127 - - - # 4-body interactions in this example are listed by atomType and bondType - # The atomIDs involved are determined automatically. The forumula used is: - # - # Udihedral(phi) = K * (1 + cos(n*phi - d)) - # - # The corresponding command is - # dihedral_coeff dihedralType charmm K d w - # - # The d parameter is in degrees, K is in kcal/mol/rad^2. - # "w" is the weight for 1-4 pair interactions, which we set to 0.0. - # This should turn off pairwise interactions between 1-4 bonded atoms - # which are also involved in any of the dihedral interactions below: - # - dihedral_coeff @dihedral:CCCC charmm -0.5 1 180 0.0 - dihedral_coeff @dihedral:RCCR charmm -1.5 1 -90 0.0 - - - # 2-body (non-bonded) interactions are listed by atom type: - - # interaction between atoms of the same type: - # epsilon signma - pair_coeff @atom:CA @atom:CA lj/charmm/coul/charmm 0.010 2.0 - pair_coeff @atom:R @atom:R lj/charmm/coul/charmm 2.50 3.6 - # - # interactions between different atom types use arithmetic mixing rules - - } # write_once("In Settings") - - - write_once("In Init") { - # -- Default styles for "2bead" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style none - pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } -} # 2bead - diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt deleted file mode 100644 index 567ec3ae5d..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/moltemplate_files/system.lt +++ /dev/null @@ -1,25 +0,0 @@ -import "peptide.lt" - - -# Specify the periodic boundary conditions: -write_once("Data Boundary") { - 0 180.0 xlo xhi - 0 180.0 ylo yhi - 0 180.0 zlo zhi -} - -# Create 27 peptides in a rectangular grid -peptides = new Peptide [3].move(0, 0, 60.0) - [3].move(0, 60.0, 0) - [3].move(60.0, 0, 0) - -# Now (for fun) shift some of the peptides -# in the x direction by a distance of 25.0 -# Suppose we want to move the middle slice -# (which has constant Z). We do that this way: -peptides[1][*][*].move(25,0,0) -# more examples: -peptides[*][1][*].move(0,0,25) -peptides[*][*][1].move(0,25,0) - - diff --git a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt deleted file mode 100644 index eb864e049e..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.nvt +++ /dev/null @@ -1,38 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# I you want to be careful, you can minimize the system first. (Try using -# "run.in.min" and uncomment the read_restart command in this file below.) -# read_restart system_after_min.rst - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 2.0 -dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve". -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) - -fix fxlan all langevin 300.0 300.0 5000.0 48279 -fix fxnve all nve - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 2500 # time interval for printing out "thermo" data - -restart 1000000 restart_nvt - -run 1000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT deleted file mode 100644 index 1a077178e3..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README.TXT +++ /dev/null @@ -1,36 +0,0 @@ -This is a very crude attempt to create a polymer melt -consisting of 150 copies of the same polymer. - -THE FORCE FIELD PARAMETERS AND CONFORMATION FOR THIS SYSTEM ARE COMPLETELY WRONG - -The purpose of this example is to demonstrate one way to create a -large number of randomly generated polymers, and to use -an NPT simulation to pack them all into a small box. -(Smaller than their initial outstretched length.) - -Each polymer is a random heteropolymer of length 200 monomers. -This polymer is a polymoer of PVDF and PCTFE monomers -selected randomly in a 1:3 ratio. -Again, this is not a realistic simulation of PVDV or PCTFE polymers, - -Furthermore, even after the simulation is done, the arrangement of the -polymers in the box is not characteristic of a truly random polymer melt. - - ----- A note on size --- - -This is a large system with nearly 200000 atoms. -It takes several minutes to compile this example -and (currently requiring at least 4.0 Gb of memory). -(I'm working on reducing that requirement. -Andrew 2012-9-12) - ------------------------ - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh deleted file mode 100755 index ac21c4c45e..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh +++ /dev/null @@ -1,14 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.nvt diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg deleted file mode 100644 index f67da797f1..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/2bead.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg deleted file mode 100644 index 15d7b29676..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/3bead.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 6915e27391..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,277 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 116 !NATOM - 1 1 3 3 0.000000 12.0000 0 - 2 1 4 4 0.000000 17.0000 0 - 3 1 4 4 0.000000 17.0000 0 - 4 1 3 3 0.000000 12.0000 0 - 5 1 4 4 0.000000 17.0000 0 - 6 1 4 4 0.000000 17.0000 0 - 7 1 1 1 0.000000 12.0000 0 - 8 1 2 2 0.000000 17.0000 0 - 9 1 1 1 0.000000 12.0000 0 - 10 1 2 2 0.000000 17.0000 0 - 11 1 1 1 0.000000 12.0000 0 - 12 1 2 2 0.000000 17.0000 0 - 13 1 3 3 0.000000 12.0000 0 - 14 1 4 4 0.000000 17.0000 0 - 15 1 4 4 0.000000 17.0000 0 - 16 1 1 1 0.000000 12.0000 0 - 17 1 2 2 0.000000 17.0000 0 - 18 1 1 1 0.000000 12.0000 0 - 19 1 2 2 0.000000 17.0000 0 - 20 1 1 1 0.000000 12.0000 0 - 21 1 2 2 0.000000 17.0000 0 - 22 1 1 1 0.000000 12.0000 0 - 23 1 2 2 0.000000 17.0000 0 - 24 1 1 1 0.000000 12.0000 0 - 25 1 2 2 0.000000 17.0000 0 - 26 1 1 1 0.000000 12.0000 0 - 27 1 2 2 0.000000 17.0000 0 - 28 1 1 1 0.000000 12.0000 0 - 29 1 2 2 0.000000 17.0000 0 - 30 1 3 3 0.000000 12.0000 0 - 31 1 4 4 0.000000 17.0000 0 - 32 1 4 4 0.000000 17.0000 0 - 33 1 1 1 0.000000 12.0000 0 - 34 1 2 2 0.000000 17.0000 0 - 35 1 3 3 0.000000 12.0000 0 - 36 1 4 4 0.000000 17.0000 0 - 37 1 4 4 0.000000 17.0000 0 - 38 1 1 1 0.000000 12.0000 0 - 39 1 2 2 0.000000 17.0000 0 - 40 1 3 3 0.000000 12.0000 0 - 41 1 4 4 0.000000 17.0000 0 - 42 1 4 4 0.000000 17.0000 0 - 43 1 3 3 0.000000 12.0000 0 - 44 1 4 4 0.000000 17.0000 0 - 45 1 4 4 0.000000 17.0000 0 - 46 1 1 1 0.000000 12.0000 0 - 47 1 2 2 0.000000 17.0000 0 - 48 1 1 1 0.000000 12.0000 0 - 49 1 2 2 0.000000 17.0000 0 - 50 1 3 3 0.000000 12.0000 0 - 51 1 4 4 0.000000 17.0000 0 - 52 1 4 4 0.000000 17.0000 0 - 53 1 1 1 0.000000 12.0000 0 - 54 1 2 2 0.000000 17.0000 0 - 55 1 1 1 0.000000 12.0000 0 - 56 1 2 2 0.000000 17.0000 0 - 57 1 3 3 0.000000 12.0000 0 - 58 1 4 4 0.000000 17.0000 0 - 59 1 4 4 0.000000 17.0000 0 - 60 1 1 1 0.000000 12.0000 0 - 61 1 2 2 0.000000 17.0000 0 - 62 1 3 3 0.000000 12.0000 0 - 63 1 4 4 0.000000 17.0000 0 - 64 1 4 4 0.000000 17.0000 0 - 65 1 1 1 0.000000 12.0000 0 - 66 1 2 2 0.000000 17.0000 0 - 67 1 1 1 0.000000 12.0000 0 - 68 1 2 2 0.000000 17.0000 0 - 69 1 1 1 0.000000 12.0000 0 - 70 1 2 2 0.000000 17.0000 0 - 71 1 3 3 0.000000 12.0000 0 - 72 1 4 4 0.000000 17.0000 0 - 73 1 4 4 0.000000 17.0000 0 - 74 1 3 3 0.000000 12.0000 0 - 75 1 4 4 0.000000 17.0000 0 - 76 1 4 4 0.000000 17.0000 0 - 77 1 1 1 0.000000 12.0000 0 - 78 1 2 2 0.000000 17.0000 0 - 79 1 1 1 0.000000 12.0000 0 - 80 1 2 2 0.000000 17.0000 0 - 81 1 3 3 0.000000 12.0000 0 - 82 1 4 4 0.000000 17.0000 0 - 83 1 4 4 0.000000 17.0000 0 - 84 1 1 1 0.000000 12.0000 0 - 85 1 2 2 0.000000 17.0000 0 - 86 1 1 1 0.000000 12.0000 0 - 87 1 2 2 0.000000 17.0000 0 - 88 1 1 1 0.000000 12.0000 0 - 89 1 2 2 0.000000 17.0000 0 - 90 1 1 1 0.000000 12.0000 0 - 91 1 2 2 0.000000 17.0000 0 - 92 1 3 3 0.000000 12.0000 0 - 93 1 4 4 0.000000 17.0000 0 - 94 1 4 4 0.000000 17.0000 0 - 95 1 1 1 0.000000 12.0000 0 - 96 1 2 2 0.000000 17.0000 0 - 97 1 1 1 0.000000 12.0000 0 - 98 1 2 2 0.000000 17.0000 0 - 99 1 1 1 0.000000 12.0000 0 - 100 1 2 2 0.000000 17.0000 0 - 101 1 3 3 0.000000 12.0000 0 - 102 1 4 4 0.000000 17.0000 0 - 103 1 4 4 0.000000 17.0000 0 - 104 1 1 1 0.000000 12.0000 0 - 105 1 2 2 0.000000 17.0000 0 - 106 1 1 1 0.000000 12.0000 0 - 107 1 2 2 0.000000 17.0000 0 - 108 1 3 3 0.000000 12.0000 0 - 109 1 4 4 0.000000 17.0000 0 - 110 1 4 4 0.000000 17.0000 0 - 111 1 1 1 0.000000 12.0000 0 - 112 1 2 2 0.000000 17.0000 0 - 113 1 1 1 0.000000 12.0000 0 - 114 1 2 2 0.000000 17.0000 0 - 115 1 1 1 0.000000 12.0000 0 - 116 1 2 2 0.000000 17.0000 0 - - 115 !NBOND: bonds - 1 2 1 3 1 4 4 5 - 4 6 4 7 7 8 7 9 - 9 10 9 11 11 12 11 13 - 13 14 13 15 13 16 16 17 - 16 18 18 19 18 20 20 21 - 20 22 22 23 22 24 24 25 - 24 26 26 27 26 28 28 29 - 28 30 30 31 30 32 30 33 - 33 34 33 35 35 36 35 37 - 35 38 38 39 38 40 40 41 - 40 42 40 43 43 44 43 45 - 43 46 46 47 46 48 48 49 - 48 50 50 51 50 52 50 53 - 53 54 53 55 55 56 55 57 - 57 58 57 59 57 60 60 61 - 60 62 62 63 62 64 62 65 - 65 66 65 67 67 68 67 69 - 69 70 69 71 71 72 71 73 - 71 74 74 75 74 76 74 77 - 77 78 77 79 79 80 79 81 - 81 82 81 83 81 84 84 85 - 84 86 86 87 86 88 88 89 - 88 90 90 91 90 92 92 93 - 92 94 92 95 95 96 95 97 - 97 98 97 99 99 100 99 101 - 101 102 101 103 101 104 104 105 - 104 106 106 107 106 108 108 109 - 108 110 108 111 111 112 111 113 - 113 114 113 115 115 116 - - 193 !NTHETA: angles - 1 4 7 38 40 43 40 43 46 - 69 71 74 71 74 77 30 33 35 - 35 38 40 57 60 62 4 7 9 - 9 11 13 13 16 18 26 28 30 - 43 46 48 46 48 50 50 53 55 - 53 55 57 62 65 67 67 69 71 - 74 77 79 77 79 81 81 84 86 - 88 90 92 92 95 97 97 99 101 - 101 104 106 104 106 108 108 111 113 - 7 9 11 16 18 20 18 20 22 - 20 22 24 22 24 26 24 26 28 - 65 67 69 84 86 88 86 88 90 - 95 97 99 111 113 115 11 13 16 - 28 30 33 33 35 38 48 50 53 - 55 57 60 60 62 65 79 81 84 - 90 92 95 99 101 104 106 108 111 - 5 4 7 6 4 7 11 13 14 - 11 13 15 14 13 16 15 13 16 - 28 30 31 28 30 32 31 30 33 - 32 30 33 33 35 36 33 35 37 - 36 35 38 37 35 38 38 40 41 - 38 40 42 44 43 46 45 43 46 - 48 50 51 48 50 52 51 50 53 - 52 50 53 55 57 58 55 57 59 - 58 57 60 59 57 60 60 62 63 - 60 62 64 63 62 65 64 62 65 - 69 71 72 69 71 73 75 74 77 - 76 74 77 79 81 82 79 81 83 - 82 81 84 83 81 84 90 92 93 - 90 92 94 93 92 95 94 92 95 - 99 101 102 99 101 103 102 101 104 - 103 101 104 106 108 109 106 108 110 - 109 108 111 110 108 111 7 9 10 - 8 7 9 9 11 12 10 9 11 - 16 18 19 17 16 18 18 20 21 - 19 18 20 20 22 23 21 20 22 - 22 24 25 23 22 24 24 26 27 - 25 24 26 26 28 29 27 26 28 - 46 48 49 47 46 48 53 55 56 - 54 53 55 65 67 68 66 65 67 - 67 69 70 68 67 69 77 79 80 - 78 77 79 84 86 87 85 84 86 - 86 88 89 87 86 88 88 90 91 - 89 88 90 95 97 98 96 95 97 - 97 99 100 98 97 99 104 106 107 - 105 104 106 111 113 114 112 111 113 - 113 115 116 114 113 115 1 4 5 - 1 4 6 2 1 4 3 1 4 - 40 43 44 40 43 45 41 40 43 - 42 40 43 71 74 75 71 74 76 - 72 71 74 73 71 74 4 7 8 - 12 11 13 13 16 17 29 28 30 - 30 33 34 34 33 35 35 38 39 - 39 38 40 43 46 47 49 48 50 - 50 53 54 56 55 57 57 60 61 - 61 60 62 62 65 66 70 69 71 - 74 77 78 80 79 81 81 84 85 - 91 90 92 92 95 96 100 99 101 - 101 104 105 107 106 108 108 111 112 - 2 1 3 5 4 6 14 13 15 - 31 30 32 36 35 37 41 40 42 - 44 43 45 51 50 52 58 57 59 - 63 62 64 72 71 73 75 74 76 - 82 81 83 93 92 94 102 101 103 - 109 108 110 - - 47 !NPHI: dihedrals - 38 40 43 46 69 71 74 77 - 1 4 7 9 40 43 46 48 - 67 69 71 74 71 74 77 79 - 35 38 40 43 30 33 35 38 - 28 30 33 35 33 35 38 40 - 57 60 62 65 55 57 60 62 - 4 7 9 11 7 9 11 13 - 13 16 18 20 24 26 28 30 - 62 65 67 69 65 67 69 71 - 81 84 86 88 86 88 90 92 - 92 95 97 99 95 97 99 101 - 108 111 113 115 16 18 20 22 - 18 20 22 24 20 22 24 26 - 22 24 26 28 84 86 88 90 - 9 11 13 16 11 13 16 18 - 26 28 30 33 46 48 50 53 - 53 55 57 60 48 50 53 55 - 60 62 65 67 77 79 81 84 - 79 81 84 86 88 90 92 95 - 90 92 95 97 97 99 101 104 - 104 106 108 111 99 101 104 106 - 106 108 111 113 43 46 48 50 - 50 53 55 57 74 77 79 81 - 101 104 106 108 - - 0 !NIMPHI: impropers - - - 0 !NDON: donors - - - 0 !NACC: acceptors - - - 0 !NNB - - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg deleted file mode 100644 index cc6822e7b3..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=0ps.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg b/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg deleted file mode 100644 index efcaa76c06..0000000000 Binary files a/tools/moltemplate/examples/CG_misc/random_heteropolymer/images/random_heteropolymer_t=1ns.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt deleted file mode 100644 index 9a90c172ae..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt +++ /dev/null @@ -1,115 +0,0 @@ - # ---------------------------------------------------------------------- - # -- General comment: -- - # -- The write() and write_once() commands create and append text to -- - # -- files (replacing variables beginning with @ or $ with counters.) -- - # -- File names beginning with "In " or "Data " are special. -- - # -- They will be pasted into the LAMMPS input script and -- - # -- data files which are generated by moltemplate. The syntax -- - # -- of these files is exactly the same as the syntax from the -- - # -- corresponding sections of a LAMMPS input script or data file. -- - # ---------------------------------------------------------------------- - - -MonomerTypes { - - - 2bead { - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.0000 - $atom:R $mol:... @atom:R 0.0 0.000 4.400 0.0000 - } - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:CR @bond:../sidechain $atom:CA $atom:R - } - - # atom-type mass - - write_once("Data Masses") { - @atom:CA 12.0 - @atom:R 17.0 - } - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.10 2.0 - pair_coeff @atom:R @atom:R 0.50 3.0 - } - - } # 2bead - - - 3bead { - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA 0.0 0.000 1.000 0.000 - $atom:R1 $mol:... @atom:R 0.0 0.000 2.700 2.950 - $atom:R2 $mol:... @atom:R 0.0 0.000 2.700 -2.950 - } - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:CR1 @bond:../sidechain $atom:CA $atom:R1 - $bond:CR2 @bond:../sidechain $atom:CA $atom:R2 - } - - # atom-type mass - - write_once("Data Masses") { - @atom:CA 12.0 - @atom:R 17.0 - } - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.10 2.0 - pair_coeff @atom:R @atom:R 0.50 3.0 - } - } # 3bead - - - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:sidechain 20.0 3.4 - bond_coeff @bond:bb 20.0 3.4 # "bb" shorthand for "backbone" - } - - # Although there's no need to define angular interactions (because this - # "molecule" only contains two atoms), we define the settings for angles - # or dihedrals which might be present later when we build a polymer. - - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:backbone 10.00 160 - angle_coeff @angle:sidechain 10.00 120 - angle_coeff @angle:RCR 10.00 120 - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbn 0.10 -0.271016 3.145034 0.0 - } - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:*/CA @atom:*/CA @atom:*/CA @bond:* @bond:* - @angle:sidechain @atom:*/CA @atom:*/CA @atom:*/R @bond:* @bond:* - @angle:RCR @atom:*/R @atom:*/CA @atom:*/R @bond:* @bond:* - } - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:*/CA @atom:*/CA @atom:*/CA @atom:*/CA * * * - } - -} # MonomerTypes - diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt deleted file mode 100644 index 9497dcc390..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/polymer.lt +++ /dev/null @@ -1,82 +0,0 @@ -import "monomers.lt" - -using namespace MonomerTypes - -RandomHeteropolymer { - - # Make a chain of monomers with random composition: - - monomers = new random([2bead,3bead], - [0.6,0.4], - 123456) # <-- optional random seed - [50].rot(180,1,0,0).move(2.95, 0, 0) - - # Now, link the monomers together this way: - - write("Data Bonds") { - $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/CA $atom:monomers[1]/CA - $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/CA $atom:monomers[2]/CA - $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/CA $atom:monomers[3]/CA - $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/CA $atom:monomers[4]/CA - $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/CA $atom:monomers[5]/CA - $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/CA $atom:monomers[6]/CA - $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/CA $atom:monomers[7]/CA - $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/CA $atom:monomers[8]/CA - $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/CA $atom:monomers[9]/CA - $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/CA $atom:monomers[10]/CA - $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/CA $atom:monomers[11]/CA - $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/CA $atom:monomers[12]/CA - $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/CA $atom:monomers[13]/CA - $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/CA $atom:monomers[14]/CA - $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/CA $atom:monomers[15]/CA - $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/CA $atom:monomers[16]/CA - $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/CA $atom:monomers[17]/CA - $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/CA $atom:monomers[18]/CA - $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/CA $atom:monomers[19]/CA - $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/CA $atom:monomers[20]/CA - $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/CA $atom:monomers[21]/CA - $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/CA $atom:monomers[22]/CA - $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/CA $atom:monomers[23]/CA - $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/CA $atom:monomers[24]/CA - $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/CA $atom:monomers[25]/CA - $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/CA $atom:monomers[26]/CA - $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/CA $atom:monomers[27]/CA - $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/CA $atom:monomers[28]/CA - $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/CA $atom:monomers[29]/CA - $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/CA $atom:monomers[30]/CA - $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/CA $atom:monomers[31]/CA - $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/CA $atom:monomers[32]/CA - $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/CA $atom:monomers[33]/CA - $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/CA $atom:monomers[34]/CA - $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/CA $atom:monomers[35]/CA - $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/CA $atom:monomers[36]/CA - $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/CA $atom:monomers[37]/CA - $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/CA $atom:monomers[38]/CA - $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/CA $atom:monomers[39]/CA - $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/CA $atom:monomers[40]/CA - $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/CA $atom:monomers[41]/CA - $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/CA $atom:monomers[42]/CA - $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/CA $atom:monomers[43]/CA - $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/CA $atom:monomers[44]/CA - $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/CA $atom:monomers[45]/CA - $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/CA $atom:monomers[46]/CA - $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/CA $atom:monomers[47]/CA - $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/CA $atom:monomers[48]/CA - $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/CA $atom:monomers[49]/CA - } - - # These lines of moltemplate script above were generated in python: - # for i in range(0,49): - # print(' $bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers[' - # +str(i)+']/CA $atom:monomers['+str(i+1)+']/CA') - - # Finally, create a molecule ID number for this large polymer object - - create_var { $mol } - -} # RandomHeteropolymer - - - -# Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomers.lt" diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt deleted file mode 100644 index 11f2d48fad..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/system.lt +++ /dev/null @@ -1,33 +0,0 @@ -# LAMMPS supports a large number of force-field styles. We must select -# which ones we need. This information belongs in the "In Init" section (and -# (you can specify it anywhere in your LT files, multiple times if you like). -# If different molecules use different force-field styles, you can use hybrid -# styles. (In this example the molecules share the same pair_style.) - -write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - pair_style lj/cut 9.0 - # If you have charged molecules immersed in a salty implicit - # solvent, you might try something like this this instead: - # pair_style lj/cut/coul/debye 0.1 9.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 -} - - -write_once("Data Boundary") { - 0.0 150.0 xlo xhi - 0.0 150.0 ylo yhi - 0.0 150.0 zlo zhi -} - - -import "polymer.lt" - -polymer = new RandomHeteropolymer - diff --git a/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt deleted file mode 100644 index 5e08f03cb2..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/run.in.nvt +++ /dev/null @@ -1,29 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - -timestep 2.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data - -fix fxlan all langevin 300.0 300.0 120 48279 -fix fxnve all nve - -# Temperature = 500 degrees - -run 500000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_misc/translocation/README.TXT b/tools/moltemplate/examples/CG_misc/translocation/README.TXT deleted file mode 100644 index b9bac96d50..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README.TXT +++ /dev/null @@ -1,23 +0,0 @@ - -This example contains a (crude and somewhat simple) example of -the translocation of a (rather short) polymer through a hole in a wall, -surrounded by an explicit LJ solvent. - -(I used a short polymer because a longer polymer would require a larger box. - But this example looked more impressive visually when I used a smaller box.) ----- -Note: You must compile LAMMPS with the optional "RIGID" package installed. To - do this, go to the "src" directory of your lammps installation and type: - make yes-RIGID - make clean-all - make NAME_OF_TARGET #<--("make ubuntu", "make g++", "make linux".) ----- - -Instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh b/tools/moltemplate/examples/CG_misc/translocation/README_run.sh deleted file mode 100755 index 7078918d5a..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh +++ /dev/null @@ -1,28 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" file is a LAMMPS input script containing -# references to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.nvt # Run a simulation at constant volume - -#or - -lmp_linux -i run.in.npt # Run a simulation at constant pressure - # (Note: Constant pressure conditions have not been - # well tested. The "run.in.npt" script may fail.) - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.nvt -#or -#mpirun -np 4 lmp_linux -i run.in.npt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh b/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 4a3f43234b..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,1995 +0,0 @@ -PSF - 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# ---------------------------------------------------------------------- - # -- General comment: -- - # -- The write() and write_once() commands create and append text to -- - # -- files (replacing variables beginning with @ or $ with counters.) -- - # -- File names beginning with "In " or "Data " are special. -- - # -- They will be pasted into the LAMMPS input script and -- - # -- data files which are generated by moltemplate. The syntax -- - # -- of these files is exactly the same as the syntax from the -- - # -- corresponding sections of a LAMMPS input script or data file. -- - # ---------------------------------------------------------------------- - - -Monomer { - - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:CA $mol:... @atom:CA 0.0 0.000 0.4000 0.00000 - $atom:R1 $mol:... @atom:R 0.0 0.000 1.000 1.000 - $atom:R2 $mol:... @atom:R 0.0 0.000 1.000 -1.000 - } - - # Note: The "..." in "$mol:..." tells moltemplate that this molecule may - # be a part of a larger molecule, and (if so) to use the larger - # parent object's molecule id number as it's own - - - # atom-type mass - - write_once("Data Masses") { - @atom:CA 13.0 - @atom:R 50.0 - } - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:CA @atom:CA 0.05 2.0 - pair_coeff @atom:R @atom:R 0.50 2.0 - } - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:CR1 @bond:sidechain $atom:CA $atom:R1 - $bond:CR2 @bond:sidechain $atom:CA $atom:R2 - } - - write_once("In Settings") { - # bond-type k r0 - bond_coeff @bond:sidechain 30.0 1.2 - bond_coeff @bond:bb 30.0 2.0 # "bb" shorthand for "backbone" - } - - # Although there's no need to define angular interactions (because this - # "molecule" only contains two atoms), we define the settings for angles - # or dihedrals which might be present later when we build a polymer. - - write_once("In Settings") { - # angle-type k theta0 - angle_coeff @angle:backbone 50.00 160 - angle_coeff @angle:sidechain 50.00 120 - angle_coeff @angle:RCR 50.00 120 - # dihedral-type K1 K2 K3 K4 - dihedral_coeff @dihedral:backbn 1.411036 -0.271016 3.145034 0.0 - } - - # Rules for determining 3 and 4-body bonded interactions by type - - # angle-type atomType1 atomType2 atomType3 bondType1 bondType2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:CA @atom:CA @atom:CA @bond:* @bond:* - @angle:sidechain @atom:CA @atom:CA @atom:R @bond:* @bond:* - @angle:RCR @atom:R @atom:CA @atom:R @bond:* @bond:* - } - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:CA @atom:CA @atom:CA @atom:CA @bond:* @bond:* @bond:* - } - -} # Monomer - - - - - - -# ------------------------------------------------------------------------- -# Heteropolymers: -# -# There is a similar example for heteropolymers which is distributed online -# bundled with the moltemplate software. It is named "2bead_heteropolymer", -# and it demonstrates how to share backbone (CA) atoms, bonds and angles -# (so that you don't have to define them seperately for each type of monomer). -# ------------------------------------------------------------------------- - diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt deleted file mode 100644 index d7ab89dc36..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/polymer.lt +++ /dev/null @@ -1,35 +0,0 @@ -import "monomer.lt" - -Polymer { - - # Make a chain of monomers - monomers = new Monomer [12].rot(180, 1,0,0).move(2.0, 0, 0) - - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:bb1 @bond:Monomer/bb $atom:monomers[0]/CA $atom:monomers[1]/CA - $bond:bb2 @bond:Monomer/bb $atom:monomers[1]/CA $atom:monomers[2]/CA - $bond:bb3 @bond:Monomer/bb $atom:monomers[2]/CA $atom:monomers[3]/CA - $bond:bb4 @bond:Monomer/bb $atom:monomers[3]/CA $atom:monomers[4]/CA - $bond:bb5 @bond:Monomer/bb $atom:monomers[4]/CA $atom:monomers[5]/CA - $bond:bb6 @bond:Monomer/bb $atom:monomers[5]/CA $atom:monomers[6]/CA - $bond:bb7 @bond:Monomer/bb $atom:monomers[6]/CA $atom:monomers[7]/CA - $bond:bb8 @bond:Monomer/bb $atom:monomers[7]/CA $atom:monomers[8]/CA - $bond:bb9 @bond:Monomer/bb $atom:monomers[8]/CA $atom:monomers[9]/CA - $bond:bb10 @bond:Monomer/bb $atom:monomers[9]/CA $atom:monomers[10]/CA - $bond:bb11 @bond:Monomer/bb $atom:monomers[10]/CA $atom:monomers[11]/CA - } - - create_var { $mol } # Create a molecule ID number for this polymer - - # This causes monomer[0], monomer[1], ... to share the same molecule counter - # because in the 2bead.lt file, the "..." in "$mol:..." preferentially looks - # for a counter of that type in a parent molecule or earlier ancestor. - -} # Polymer - - - -# Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomer.lt" diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt deleted file mode 100644 index 1073a58a14..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent.lt +++ /dev/null @@ -1,23 +0,0 @@ -###################### SOLVENT ######################### - -import "solvent_single.lt" - -# Fill the simulation box with a solvent. -# In this example, the solvent is made of many -# copies of "MoleculeA" (which has only one atom). - -solvent = new MoleculeA [12].move(3.0,0,0) - [12].move(0,3.0,0) - [12].move(0,0,3.0) - -# To start with a reasonable conformation, it's a good idea to delete the -# solvent where the walls or the polymer is going to be. Here we do it manually: - -delete solvent[*][*][2] # <-- 1st wall will go here -delete solvent[*][*][8] # <-- 2nd wall will go here -delete solvent[6-7][0-8][5-6] # <-- polymer will go here - -# Alternate notation: -# [a:b] notation also works, however the "b" is a strict upper bound... -# ...hence the last line is equivalent to "delete solvent[6:8][0:9][5:7]" -# [a*b] notation also works, and is equivalent to [a-b] diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt deleted file mode 100644 index 8057e3c6fc..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/solvent_single.lt +++ /dev/null @@ -1,22 +0,0 @@ -# The two files "solvent_single.lt" and "wall_single.lt" -# define two very simple molecules containing one atom each. -# Both atoms have a similar size (the have the same sigma parameter). - - -MoleculeA { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:a $mol:. @atom:a 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:a 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:a @atom:a 0.60 3.0 7.5 #<--attractive - group groupA type @atom:a #(Atoms of this type belong to the "A" group) - } - -} - diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt deleted file mode 100644 index 90d60d3baa..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt +++ /dev/null @@ -1,55 +0,0 @@ - -# LAMMPS supports a large number of force-field styles. We must select -# which ones we need. This information belongs in the "In Init" section (and -# (you can specify it anywhere in your LT files, multiple times if you like). -# If different molecules use different force-field styles, you can use hybrid -# styles. (In this example the molecules share the same pair_style.) - -write_once("In Init") { - units real - atom_style full - bond_style harmonic - angle_style harmonic - dihedral_style opls - pair_style lj/cut 9.0 - # If you have charged molecules immersed in a salty implicit - # solvent, you might try something like this this instead: - # pair_style lj/cut/coul/debye 0.1 9.0 - pair_modify mix arithmetic - dielectric 80.0 - special_bonds lj 0.0 0.0 0.0 -} - - -write_once("Data Boundary") { - 0.0 36.0 xlo xhi - 0.0 36.0 ylo yhi - 0.0 36.0 zlo zhi -} - - -import "solvent.lt" - -import "walls.lt" - -import "polymer.lt" - -polymer = new Polymer -polymer.rot(-90.0, 0,0,1) # rotate it -90 degrees around the Y axis -polymer.move(19.5,22.5,16.5) # move it near the openning of the hole - - - -####################### Notes: ######################### -# -# In this example we deleted solvent and wall molecule objects. -# You can also delete a monomer inside the polymer. To do that use: -# delete polymer/monomers[6] -# You can also delete individual atoms, bonds, angles, dihedrals, & impropers -# from existing molecules. For example to delete an atom in the middle -# of the polymer try this. (Bonds and other interactions will also be removed.) -# delete polymer/monomers[6]/CA -# To delete a bond, try this -# delete polymer/bb6 -# Note: This will not delete the angular interactions. Delete them manually -# Note: In both cases the two molecule fragments will keep the same mol counter. diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt deleted file mode 100644 index 79275a06b4..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/wall_single.lt +++ /dev/null @@ -1,21 +0,0 @@ -# The two files "solvent_single.lt" and "wall_single.lt" -# define two very simple molecules containing one atom each. -# Both atoms have a similar size (the have the same sigma parameter). - -MoleculeB { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:b $mol:. @atom:b 0.0 0.0 0.0 0.0 - } - write_once("Data Masses") { - @atom:b 10.0 - } - write_once("In Settings") { - # i j epsilon sigma cutoff - pair_coeff @atom:b @atom:b 0.05 3.0 7.5 #<--repulsive (approximately) - group groupB type @atom:b #(Atoms of this type belong to the "B" group) - } - -} - diff --git a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt b/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt deleted file mode 100644 index dcccac941e..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/walls.lt +++ /dev/null @@ -1,23 +0,0 @@ -####################### WALLS ########################## - -import "wall_single.lt" - -# Create a wall at position z=6.0 (6.0 = 2*3.0) - -wall1 = new MoleculeB [12].move(3.0, 0, 0) - [12].move(0, 3.0, 0) - -wall1[*][*].move(0,0,6.0) - -# Create a second wall at position z=24.0 (24.0 = 8*3.0) - -wall2 = new MoleculeB [12].move(3.0, 0, 0) - [12].move(0, 3.0, 0) - -wall2[*][*].move(0,0,24.0) - -# Now delete some of the molecules in "wall2" to create a hole. - -delete wall2[6-7][6-9] -delete wall2[5-8][7-8] - diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt b/tools/moltemplate/examples/CG_misc/translocation/run.in.npt deleted file mode 100644 index 1fb9ec9615..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt +++ /dev/null @@ -1,70 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 1.0 -dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - - -velocity groupB zero angular -velocity groupB zero linear -# (I'm not sure if the two lines above are necessary, but they don't hurt.) - -# Only the groupB atoms are immobile. - -group mobile subtract all groupB - -# ------------------------- NPT --------------------------- - -# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction - -fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile - -# ------ CONTROVERSIAL (see below): ------ - -fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 500 500 1000.0 force * off off off torque * off off off dilate mobile - -# -- Alternate npt rigid method -- -# I'm not sure which way is more correct, however -# this also seems to behave in a reasonable-looking way: -#fix Ffreezestuff groupB rigid single force * off off off torque * off off off dilate mobile -# -# The use of either "fix rigid" or "fix rigid/npt" to immobilize -# an object is somewhat controversial. Feel free to omit it. -#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing -#molecules, but I noticed that at NPT, it does a better job of maintaining -# the correct volume. However "fix rigid" has changed since then (2011), -# so this may no longer be true. Please use this example with caution.) -# ---------------------------------------- - -# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the -# forces between immobilized atoms. -neigh_modify exclude group groupB groupB - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp -compute pressMobile all pressure tempMobile - -thermo_style custom step c_tempMobile c_pressMobile temp press vol - -fix_modify fMoveStuff temp tempMobile - -run 60000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt deleted file mode 100644 index 8ef52b1ed9..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt +++ /dev/null @@ -1,44 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 1.0 -dump 1 all custom 100 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 100 # time interval for printing out "thermo" data - - -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms. (Note: This is not optional under NPT conditions.) -neigh_modify exclude group groupB groupB - -# Only the groupB atoms are immobile. -group mobile subtract all groupB - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp -compute pressMobile all pressure tempMobile - -# Integrate the equations of motion: -fix fMoveStuff mobile nvt temp 300.0 300.0 100.0 -fix_modify fMoveStuff temp tempMobile - - -run 200000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT deleted file mode 100644 index 33eeddda6e..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README.TXT +++ /dev/null @@ -1,28 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "MANYBODY" package. -# As of 2012-9, it is included by default, but this may change in the future. -# If lammps complains of a missing pair style enter "make yes-MANYBODY" -# into the shell before compiling lammps. For details see: -# http://lammps.sandia.gov/doc/Section_start.html#start_3 -This is a relatively complex example containing two different types of -molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. - -The cyclododecane molecule uses the -TraPPE force field for hydrocarbon chains. -The parameters for the TraPPE force field are -in a file named "trappe1998.lt" which should be -located in the MOLTEMPLATE_PATH. -(See moltemplate installation instructions.) - -The water solvent is implemented using the 3-body single-particle -coarse-grained "mW" water model: -Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 - -More detailed instructions on how to build LAMMPS input files and -run a short simulation are provided in other README files. - -step 1) -README_setup.sh - -step 2) -README_run.sh diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh deleted file mode 100755 index 8220a755c4..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, system.in.sw -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh deleted file mode 100755 index cb4d908984..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_setup.sh +++ /dev/null @@ -1,25 +0,0 @@ - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt - - # Here we just want to make sure that the "mW" atom type is assigned to - # number "1". It should be by default, so usually you can leave out - # -a "@atom:/WatMW/mW 1". - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg deleted file mode 100644 index 5123dc7f60..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg deleted file mode 100644 index 4003ac5f06..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=400ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg deleted file mode 100644 index f1dd1467cb..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclododecane+watMW_t=50ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg deleted file mode 100644 index 6591b236a3..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg deleted file mode 100644 index 9b4ca06fb8..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/cyclopentane_unrelaxed.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 97a19f0ffb..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,3669 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 2496 !NATOM - 1 1 1 1 0.000000 18.0200 0 - 2 2 1 1 0.000000 18.0200 0 - 3 3 1 1 0.000000 18.0200 0 - 4 4 1 1 0.000000 18.0200 0 - 5 5 1 1 0.000000 18.0200 0 - 6 6 1 1 0.000000 18.0200 0 - 7 7 1 1 0.000000 18.0200 0 - 8 8 1 1 0.000000 18.0200 0 - 9 9 1 1 0.000000 18.0200 0 - 10 10 1 1 0.000000 18.0200 0 - 11 11 1 1 0.000000 18.0200 0 - 12 12 1 1 0.000000 18.0200 0 - 13 13 1 1 0.000000 18.0200 0 - 14 14 1 1 0.000000 18.0200 0 - 15 15 1 1 0.000000 18.0200 0 - 16 16 1 1 0.000000 18.0200 0 - 17 17 1 1 0.000000 18.0200 0 - 18 18 1 1 0.000000 18.0200 0 - 19 19 1 1 0.000000 18.0200 0 - 20 20 1 1 0.000000 18.0200 0 - 21 21 1 1 0.000000 18.0200 0 - 22 22 1 1 0.000000 18.0200 0 - 23 23 1 1 0.000000 18.0200 0 - 24 24 1 1 0.000000 18.0200 0 - 25 25 1 1 0.000000 18.0200 0 - 26 26 1 1 0.000000 18.0200 0 - 27 27 1 1 0.000000 18.0200 0 - 28 28 1 1 0.000000 18.0200 0 - 29 29 1 1 0.000000 18.0200 0 - 30 30 1 1 0.000000 18.0200 0 - 31 31 1 1 0.000000 18.0200 0 - 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2425 2426 2425 2436 2426 2427 2427 2428 - 2428 2429 2429 2430 2430 2431 2431 2432 - 2432 2433 2433 2434 2434 2435 2435 2436 - 2437 2438 2437 2448 2438 2439 2439 2440 - 2440 2441 2441 2442 2442 2443 2443 2444 - 2444 2445 2445 2446 2446 2447 2447 2448 - 2449 2450 2449 2460 2450 2451 2451 2452 - 2452 2453 2453 2454 2454 2455 2455 2456 - 2456 2457 2457 2458 2458 2459 2459 2460 - 2461 2462 2461 2472 2462 2463 2463 2464 - 2464 2465 2465 2466 2466 2467 2467 2468 - 2468 2469 2469 2470 2470 2471 2471 2472 - 2473 2474 2473 2484 2474 2475 2475 2476 - 2476 2477 2477 2478 2478 2479 2479 2480 - 2480 2481 2481 2482 2482 2483 2483 2484 - 2485 2486 2485 2496 2486 2487 2487 2488 - 2488 2489 2489 2490 2490 2491 2491 2492 - 2492 2493 2493 2494 2494 2495 2495 2496 - - 768 !NTHETA: angles - 1729 1730 1731 1729 1740 1739 1730 1729 1740 - 1730 1731 1732 1731 1732 1733 1732 1733 1734 - 1733 1734 1735 1734 1735 1736 1735 1736 1737 - 1736 1737 1738 1737 1738 1739 1738 1739 1740 - 1741 1742 1743 1741 1752 1751 1742 1741 1752 - 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2270 2271 2272 2271 2272 2273 2272 2273 2274 - 2273 2274 2275 2274 2275 2276 2275 2276 2277 - 2276 2277 2278 2277 2278 2279 2278 2279 2280 - 2281 2282 2283 2281 2292 2291 2282 2281 2292 - 2282 2283 2284 2283 2284 2285 2284 2285 2286 - 2285 2286 2287 2286 2287 2288 2287 2288 2289 - 2288 2289 2290 2289 2290 2291 2290 2291 2292 - 2293 2294 2295 2293 2304 2303 2294 2293 2304 - 2294 2295 2296 2295 2296 2297 2296 2297 2298 - 2297 2298 2299 2298 2299 2300 2299 2300 2301 - 2300 2301 2302 2301 2302 2303 2302 2303 2304 - 2305 2306 2307 2305 2316 2315 2306 2305 2316 - 2306 2307 2308 2307 2308 2309 2308 2309 2310 - 2309 2310 2311 2310 2311 2312 2311 2312 2313 - 2312 2313 2314 2313 2314 2315 2314 2315 2316 - 2317 2318 2319 2317 2328 2327 2318 2317 2328 - 2318 2319 2320 2319 2320 2321 2320 2321 2322 - 2321 2322 2323 2322 2323 2324 2323 2324 2325 - 2324 2325 2326 2325 2326 2327 2326 2327 2328 - 2329 2330 2331 2329 2340 2339 2330 2329 2340 - 2330 2331 2332 2331 2332 2333 2332 2333 2334 - 2333 2334 2335 2334 2335 2336 2335 2336 2337 - 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2468 2469 2470 2469 2470 2471 2470 2471 2472 - 2473 2474 2475 2473 2484 2483 2474 2473 2484 - 2474 2475 2476 2475 2476 2477 2476 2477 2478 - 2477 2478 2479 2478 2479 2480 2479 2480 2481 - 2480 2481 2482 2481 2482 2483 2482 2483 2484 - 2485 2486 2487 2485 2496 2495 2486 2485 2496 - 2486 2487 2488 2487 2488 2489 2488 2489 2490 - 2489 2490 2491 2490 2491 2492 2491 2492 2493 - 2492 2493 2494 2493 2494 2495 2494 2495 2496 - - 768 !NPHI: dihedrals - 1729 1730 1731 1732 1738 1739 1740 1729 - 1730 1729 1740 1739 1730 1731 1732 1733 - 1740 1729 1730 1731 1731 1732 1733 1734 - 1732 1733 1734 1735 1733 1734 1735 1736 - 1734 1735 1736 1737 1735 1736 1737 1738 - 1736 1737 1738 1739 1737 1738 1739 1740 - 1741 1742 1743 1744 1750 1751 1752 1741 - 1742 1741 1752 1751 1742 1743 1744 1745 - 1752 1741 1742 1743 1743 1744 1745 1746 - 1744 1745 1746 1747 1745 1746 1747 1748 - 1746 1747 1748 1749 1747 1748 1749 1750 - 1748 1749 1750 1751 1749 1750 1751 1752 - 1753 1754 1755 1756 1762 1763 1764 1753 - 1754 1753 1764 1763 1754 1755 1756 1757 - 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0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg deleted file mode 100644 index 0ac8c2c011..0000000000 Binary files a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/images/watMW.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh deleted file mode 100755 index 97b9f577d9..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/README.sh +++ /dev/null @@ -1,11 +0,0 @@ -# Use this command to generate the LAMMPS input files: - -moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt - -# The -a argument insures that the "mW" atom type is assigned to "1". -# (This is necessary for the pair_coeff command to work. -# See system.lt for details.) - -# Note: To get rid of the annoying "atom_style unspecified warnings, -# use the "-atomstyle" command line argument, as in: -# moltemplate.sh -atomstyle full -a "@atom:/WatMW/mW 1" system.lt diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt deleted file mode 100644 index ceaa1c69d8..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/cyclododecane.lt +++ /dev/null @@ -1,55 +0,0 @@ -import "trappe1998.lt" - -# The "trappe1998.lt" file is usually located in $MOLTEMPLATE_PATH (and is -# distributed with moltemplate. See the "Installation" section in the manual.) -# It contains definitions of the atoms "CH2", "CH3", and "CH4", as well -# as "saturated" bonds, and the parameters for (bonded/nonbonded) -# interactions between these atoms (all enclosed within the "TraPPE" namespace). - - -Cyclododecane { - - write('Data Atoms') { - $atom:C1 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.94118 0.0 - $atom:C2 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 1.47059 - $atom:C3 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 2.54714 - $atom:C4 $mol:. @atom:TraPPE/CH2 0.0 0.00000 0.0 2.94118 - $atom:C5 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 2.54714 - $atom:C6 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 1.47059 - $atom:C7 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.94118 0.0 - $atom:C8 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -2.54714 -1.47059 - $atom:C9 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -1.47059 -2.54714 - $atom:C10 $mol:. @atom:TraPPE/CH2 0.0 0.00000 -0.0 -2.94118 - $atom:C11 $mol:. @atom:TraPPE/CH2 0.0 0.00000 1.47059 -2.54714 - $atom:C12 $mol:. @atom:TraPPE/CH2 0.0 0.00000 2.54714 -1.47059 - } - - # The "." in "$mol:." refers to the current object's molecule ID, - # and "@atom:TraPPE/CH2" refers to the "CH2" atom-type defined in TraPPE - - write('Data Bonds') { - $bond:bond1 @bond:TraPPE/saturated $atom:C1 $atom:C2 - $bond:bond2 @bond:TraPPE/saturated $atom:C2 $atom:C3 - $bond:bond3 @bond:TraPPE/saturated $atom:C3 $atom:C4 - $bond:bond4 @bond:TraPPE/saturated $atom:C4 $atom:C5 - $bond:bond5 @bond:TraPPE/saturated $atom:C5 $atom:C6 - $bond:bond6 @bond:TraPPE/saturated $atom:C6 $atom:C7 - $bond:bond7 @bond:TraPPE/saturated $atom:C7 $atom:C8 - $bond:bond8 @bond:TraPPE/saturated $atom:C8 $atom:C9 - $bond:bond9 @bond:TraPPE/saturated $atom:C9 $atom:C10 - $bond:bond10 @bond:TraPPE/saturated $atom:C10 $atom:C11 - $bond:bond11 @bond:TraPPE/saturated $atom:C11 $atom:C12 - $bond:bond12 @bond:TraPPE/saturated $atom:C12 $atom:C1 - } - -} # Cyclododecane - - -# coordinates in the "Data Atoms" section generated by this python code: -# from math import * -# bond_length=1.54 -# N=12 -# R=(N*bond_length)/(2*pi) -# for i in range(0,N): -# print('$atom:C'+str(i+1)+' $mol:... @atom:TraPPE/CH2 0.0 0.00000 '+ -# str(round(R*cos(i*2*pi/N),5))+' '+str(round(R*sin(i*2*pi/N),5))) diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt deleted file mode 100644 index 4a7063491b..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/system.lt +++ /dev/null @@ -1,62 +0,0 @@ -# This is a relatively complex example containing two different types of -# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. - -import "watmw.lt" -import "cyclododecane.lt" - -write_once("Data Boundary") { - 0.000000 48.000 xlo xhi - 0.000000 48.000 ylo yhi - 0.000000 48.000 zlo zhi -} - -wat = new WatMW [12].move(0, 0, 4.0) - [12].move(0, 4.0, 0) - [12].move(4.0, 0, 0) - -cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) - [4].move(0, 12.0, 0) - [4].move(12.0, 0, 0) - -# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) -cyclododecane[*][*][*].move(6.0,6.0,6.0) - -write_once("In Init") { - # -- Tell LAMMPS we want to use two different pair styles - # -- (This overrides earlier settings.) - pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 -} - - -write_once("In Settings") { - # -- Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) -} - - - -# -- Somewhere we must eventually define interactions -# -- between atoms from different molecule types - -write_once("In Settings") { - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 -} - - - diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt deleted file mode 100644 index 9bcc80cb1c..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/trappe1998.lt +++ /dev/null @@ -1,50 +0,0 @@ -# This file stores complete LAMMPS data for the TraPPE model of saturated -# hydrocarbon chains. In this "united-atom" model, each methyl group is -# represented by a single atom. Forces between "atoms" are taken from the -# TraPPE force-field. (J Phys Chem B, 1998, volume 102, pp.2569-2577) - -TraPPE { - - write_once("In Init") { - # -- Default styles for "TraPPE" -- - units real - atom_style full - # (Hybrid force field styles were used for portability.) - bond_style hybrid harmonic - angle_style hybrid harmonic - dihedral_style hybrid opls - improper_style none - pair_style hybrid lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - @atom:CH4 16.3307 - } - - write_once("Data Angles By Type") { - @angle:backbone @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated - } - - write_once("Data Dihedrals By Type") { - @dihedral:backbone @atom:CH? @atom:CH? @atom:CH? @atom:CH? @bond:saturated @bond:saturated @bond:saturated - } - - write_once("In Settings") { - pair_coeff @atom:CH2 @atom:CH2 lj/charmm/coul/charmm 0.091411522 3.95 - pair_coeff @atom:CH3 @atom:CH3 lj/charmm/coul/charmm 0.194746286 3.75 - pair_coeff @atom:CH4 @atom:CH4 lj/charmm/coul/charmm 0.294106636 3.73 - bond_coeff @bond:saturated harmonic 120.0 1.54 - angle_coeff @angle:backbone harmonic 62.0022 114 - dihedral_coeff @dihedral:backbone opls 1.411036 -0.271016 3.145034 0.0 - } - - write_once("In Settings") { - group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 - } - -} # class TraPPE - diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt deleted file mode 100644 index 34bdfead77..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/version_more_comments/system.lt +++ /dev/null @@ -1,80 +0,0 @@ -# This is a relatively complex example containing two different types of -# molecules, and a hybrid of Lennard-Jones and 3-body SW "pair" styles. - -import "watmw.lt" -import "cyclododecane.lt" - -write_once("Data Boundary") { - 0.000000 48.000 xlo xhi - 0.000000 48.000 ylo yhi - 0.000000 48.000 zlo zhi -} - -wat = new WatMW [12].move(0, 0, 4.0) - [12].move(0, 4.0, 0) - [12].move(4.0, 0, 0) - -cyclododecane = new Cyclododecane [4].move(0, 0, 12.0) - [4].move(0, 12.0, 0) - [4].move(12.0, 0, 0) - -# (Move them by (6.0,6.0,6.0) to avoid overlap with the water.) -cyclododecane[*][*][*].move(6.0,6.0,6.0) - -write_once("In Init") { - # -- Tell LAMMPS we want to use two different pair styles - # -- (This overrides earlier settings.) - pair_style hybrid sw lj/charmm/coul/charmm 9.0 11.0 9.0 11.0 -} - - - -write_once("In Settings") { - # -- Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # - # For this to work, the first atom type (assigned to "1") - # must refer to the "mW" atom type (defined in watmw.lt). - # (This is why we included "watmw.lt" first, to insure that the - # atom counters in WatMW are assinged first, starting with 1.) - # Alternately we can further insure that this happens, it's - # a good idea to run moltemplate.sh using the "-a" argument: - # moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt - # This assigns the atom type named @atom:/WatMW/mW to 1 -} - - - - -# -- Somewhere we must eventually define interactions -# -- between atoms from different molecule types -# -- Now define interactions between DIFFERENT molecules -# Note: In the SPC/E model, the epsilon,sigma parameters for water is 0.1553 -# 3.166. As a crude guess, I chose the LJ parameters for the interaction -# between water & the CH2,CH3,CH4 atoms using Lorentz-Berthelot mixing rules - -write_once("In Settings") { - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH2 lj/charmm/coul/charmm 0.11914784667210733 3.558 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH3 lj/charmm/coul/charmm 0.17390830404497651 3.458 - pair_coeff @atom:WatMW/mW @atom:TraPPE/CH4 lj/charmm/coul/charmm 0.21371654257637612 3.448 -} - - - - - - - - - diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt deleted file mode 100644 index c7aaecebbc..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/moltemplate_files/watmw.lt +++ /dev/null @@ -1,54 +0,0 @@ -# This file stores LAMMPS data for the "mW" water model. -# (Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016) -# -# In this model, each water molecule is represented by a single "mW" particle. -# These particles interact with their neighbors via 3-body Stillinger-Weber -# forces whose parameters are tuned to mimic directional hydrogen-bonding -# in liquid water (as well as hexagonal ice, type II ice, and -# low-density super-cooled liquid/amorphous water phases). - -WatMW { - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - write_once("system.in.sw") { - mW mW mW 6.189 2.3925 1.8 23.15 1.2 -0.333333333 7.049556277 0.602224558 4 0 0 - } - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # --Now indicate which atom type(s) are simulated using the "sw" pair style - # -- In this case only one of the atom types is used (the mW water "atom"). - - pair_coeff * * sw system.in.sw mW NULL NULL NULL - - # -- Unfortunately LAMMPS itself does not understand molemlate syntax, so - # -- the atoms are identified by order in the list, not by name. (The "mW" - # -- refers to to an identifier in the system.in.sw file, not watmw.lt.) - # -- This command says that the first atom type corresponds to the "mW" - # -- atom in system.in.sw, and to ignore the remaining three atom types - # -- (correspond to the CH2, CH3, CH4 atom types defined in trappe1998.lt. - # -- We don't want to use the "sw" force field for interactions involving - # -- these atom types, so we put "NULL" there.) - # -- Note: For this to work, you should probably run moltemplate this way: - # -- moltemplate.sh -a "@atom:WatMW/mW 1" system.lt - # -- This assigns the atom type named @atom:WatMW/mW to 1 (the first atom) - } - - # -- optional -- - - write_once("In Settings") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt deleted file mode 100644 index 59d5ce9f87..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt +++ /dev/null @@ -1,58 +0,0 @@ -# run.in.npt -# -# -- Usage -- -# -# lmp_g++ -i run.in.npt -# (assuming lmp_g++ is the name of your lammps binary) -# -# -- Prerequisite Input Files: -- -# systen.data, system.in.init, system.in.settings, system.in.sw -# -# You can generate these files with this command: -# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt -# --------------------------------- - -# ----- Init Section ----- - - -include system.in.init - - -# ----- Atom Definition Section ----- - - -read_data system.data - - -# ----- Settings Section ----- - - -include system.in.settings - - -# ----- Run Section ----- - - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. - -minimize 1.0e-5 1.0e-7 100000 400000 - - -# -- simulation protocol -- - - -timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water -dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - -run 200000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt deleted file mode 100644 index 9d499517dc..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt +++ /dev/null @@ -1,78 +0,0 @@ -# run.in.nvt -# -# -- Usage -- -# -# lmp_g++ -i run.in.nvt -# (assuming lmp_g++ is the name of your lammps binary) -# -# -- Prerequisite Input Files: -- -# systen.data, system.in.init, system.in.settings, system.in.sw -# -# You can generate these files with this command: -# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt -# --------------------------------- - - -# -- init section -- - - -include system.in.init - - - -# -- atom definition section -- - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Otherwise try "read_dump", "dump2data.py", or "restart2data". - - -read_data system.data - - - -# -- settings section -- - - -include system.in.settings - - -# -- run section -- - - -timestep 2.0 -dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz -dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - -# The following commands are useful if you want to calculate the distribution -# of alkane-chain radius-of-gyration at a given temperature & pressure. -#compute cRg TraPPE gyration -#variable vRg equal c_cRg -#compute cPE all pe -#variable vPE equal c_cPE -#fix FprintPE all print 1000 "${vPE}" file U.dat -#fix FprintRg all print 1000 "${vRg}" file Rg.dat - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data -#thermo_modify flush yes - -restart 100000 restart_nvt - -run 1000000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/README.TXT b/tools/moltemplate/examples/README.TXT deleted file mode 100644 index 0ecddbbbd4..0000000000 --- a/tools/moltemplate/examples/README.TXT +++ /dev/null @@ -1,24 +0,0 @@ -These are examples for the "moltemplate" molecule builder for LAMMPS. -http://www.moltemplate.org - -Each directory contains one or more examples. - -Each example directory contains: - - images/ This folder has pictures of the molecules in the system - moltemplate_files/ This folder contains LT files and other auxiliary files - README_setup.sh Instructions for how to use moltemplate (executable) - README_visualize.txt Instructions for viewing in DATA/DUMP files in VMD - - ...and one or more LAMMPS input scripts with names like - - run.in.min - run.in.npt - run.in.nvt - -You can run these scripts using - lmp_linux -i run.in.npt -(The name of your lammps binary, "lmp_linux" in this example, may vary. - Sometimes, these scripts must be run in a certain order. For example - it may be necessary to run run.in.min to minimize the system before - you can run the other scripts. These files have not been optimized.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT deleted file mode 100644 index 355fe42831..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README.TXT +++ /dev/null @@ -1,54 +0,0 @@ -NOTE: This example requires the "Al99.eam.alloy" file. - (It was not included in this directory because if its large size.) - As of 2012-11, I was able to obtain it here: - http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - Copy it to the directory containing this README file. ------------------------------------------------------------------------- -This example shows an alternative way to setup the -aluminum crystal loading simulation described here: -http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression -by Mark Tschopp and Nathan R. Rhodes -For additional backgroumd information, please consult that web page. - -In this example, I use moltemplate to build a "DATA" file for this system. -(I can't think of a compelling reason to do this for simple simulations like -this. But this approach might be useful if you want to artificially create -unusual structures out of aluminum crystals, or mix them with other molecules. -I created this example in response to a user request.) - - - --- To build the system --- - -Carry out the instructions in README_setup.sh, -to generate the LAMMPS DATA file and input scripts you need: -system.data, system.in.init, system.in.settings. -(The run.in script contains references to these files.) - - - --- To run LAMMPS, try a command like: --- - -lmp_linux -i run.in - - or (if you have mpi installed) - -mpirun -np 4 lmp_linux -i run.in - -This will create an ordinary LAMMPS dump file you can visualize with VMD -traj.lammpstrj (See README_visualize.txt) - -It will also create a number of other files, such as: -dump.comp_0.cfg -dump.comp_500.cfg -dump.comp_20000.cfg -Al_comp_100.def1.txt - -The dump.comp_*.cfg files can be visualized using -AtomEye if you have AtomEye and ImageJ installed. -The procedure for doing this is explained in the original tutorial at: -http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - -The "Al_comp_100.def1.txt" file is a four-column text file containing: -column 1: v_strain = (lx - v_L0)/v_L0 -column 2: -pxx/10000 (diagonal components of the stress tensor) -column 3: -pyy/10000 -column 4: -pzz/10000 diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh deleted file mode 100755 index 22eb8c4357..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # We will also need the "Al99.eam.alloy" file: - #cp -f Al99.eam.alloy ../ - # This file was (can be) downloaded from: - # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg deleted file mode 100644 index bf07914dac..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCell_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg deleted file mode 100644 index 8650cf5cb0..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=0steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg deleted file mode 100644 index 582cf5fe6d..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/images/AlCrystal10x10x10_t=20000steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh deleted file mode 100755 index 64f350f641..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/README.sh +++ /dev/null @@ -1,22 +0,0 @@ -# This example shows an alternative way to setup the -# aluminum crystal loading simulation described here: -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression -# by Mark Tschopp and Nathan R. Rhodes -# For additional backgroumd information, please consult that web page. -# -# In this example, I use moltemplate to build a "DATA" file for this system. -# (I can't think of a compelling reason to do this for simple simulations like -# this. But this approach might be useful if you want to artificially create -# unusual structures out of aluminum crystals, or mix them with other molecules. -# I created this example in response to a user request.) -# -# Use these commands to generate the LAMMPS input script and data file: - -moltemplate.sh system.lt - -# This will generate system.data, system.in.init, system.in.settings. -# In addition to will need to download "Al99.eam.alloy" file. -# (It was not included in this directory because if its large size.) -# As of 2012-11, I was able to obtain it here: -# http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt deleted file mode 100644 index f813c6f662..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/moltemplate_files/system.lt +++ /dev/null @@ -1,35 +0,0 @@ - -import "al_cell.lt" # <- this defines the unit cell for aluminum - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 40.50 xlo xhi - 0.0 40.50 ylo yhi - 0.0 40.50 zlo zhi -} - -# The next command generates an array of 10x10x10 AlCell unit cells with -# spacing 4.05 Angstroms. - -unitcells = new AlCell [10].move(0.00, 0.00, 4.05) - [10].move(0.00, 4.05, 0.00) - [10].move(4.05, 0.00, 0.00) - - - - - - - - - - - - -################################################################ -# The next command is not necessary: -# - create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # Molecule ID numbers are not necessary. Ignore this. -# diff --git a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in b/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in deleted file mode 100644 index 677cc60cab..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/aluminum_crystal_strain/run.in +++ /dev/null @@ -1,76 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- -# -# The run-settings below were stolen from: -# -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - - -compute csym all centro/atom fcc -compute peratom all pe/atom - -# EQUILIBRATION -reset_timestep 0 -timestep 0.001 -velocity all create 300 12345 mom yes rot no -fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 - -# Set thermo output -thermo 1000 -thermo_style custom step lx ly lz press pxx pyy pzz pe temp - -# Run for at least 10 picosecond (assuming 1 fs timestep) -run 20000 -unfix 1 - -# Store final cell length for strain calculations -variable tmp equal "lx" -variable L0 equal ${tmp} -print "Initial Length, L0: ${L0}" - -###################################### -# DEFORMATION -reset_timestep 0 - -fix 1 all npt temp 300 300 1 y 0 0 1 z 0 0 1 drag 1 -variable srate equal 1.0e10 -variable srate1 equal "-v_srate / 1.0e12" -fix 2 all deform 1 x erate ${srate1} units box remap x - -# Output strain and stress info to file -# for units metal, pressure is in [bars] = 100 [kPa] = 1/10000 [GPa] -# p2, p3, p4 are in GPa -variable strain equal "(lx - v_L0)/v_L0" -variable p1 equal "v_strain" -variable p2 equal "-pxx/10000" -variable p3 equal "-pyy/10000" -variable p4 equal "-pzz/10000" -fix def1 all print 100 "${p1} ${p2} ${p3} ${p4}" file Al_comp_100.def1.txt screen no - -# Use cfg for AtomEye -dump dAtomEye all cfg 250 dump.comp_*.cfg id type xs ys zs c_csym c_peratom fx fy fz -dump_modify dAtomEye element Al - -# For users without AtomEye (like me), I decided to create a regular dump file: -dump dCoords all custom 250 traj.lammpstrj id type x y z ix iy iz - -# Display thermo -thermo 1000 -thermo_style custom step v_strain temp v_p2 v_p3 v_p4 ke pe press - -run 20000 - -###################################### -# SIMULATION DONE -print "All done" diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT deleted file mode 100644 index 80ab9c443e..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_FIRST.TXT +++ /dev/null @@ -1,83 +0,0 @@ -########################################################### -# Interaction of a carbon nanotube with a pair of "mystery -# molecules" (extracted from the cnat-cnt.data/in files). -########################################################### -# Author: Aysun Itai and Andrew Jewett - -This example uses "ltemplify.py" to create molecule templates out -of two different molecules in a pre-existing LAMMPS IN/DATA file. -Then I show how to use "moltemplate.sh" to make copies of these -molecules and to move and rotate them (creating new LAMMPS IN/DATA files). - - Disclaimer: -The molecules in this example are not physically realistic. -The purpose of this example is to demonstrate ltemplify usage. - - REQUIRED INPUT FILES - -cnad-cnt.data cnad-cnt.in system.lt - - cnad-cnt.data - This is a LAMMPS data file containing the coordinates and the topology - for a system combining the two molecules together. ltemplify will extract - molecules from this file, one at a time. - - cnad-cnt.in - This file contains force-field parameters and old run settings for the system. - (We ignore the run settings in this file.) The force-field parameters in - the "cnad-cnt.in" file are only necessary because we are going to build - a completely new set of simulation input files. (We are not only going to - rotate them and duplicate the molecules.) ltemplify.py will extract the - force field parameters from this file. This approach allows us to combine - these molecules with other types of molecules later on.) - - system.lt - The "system.lt" contains the instructions what we will do with these molecules - after ltemplify.py has converted them into .LT format. In this example - it contains instructions for rotating and copying the two molecules, - (It also defines the periodic boundary conditions.) - - OUTPUT FILES - -cnad.lt -cnt.lt - -These files are referenced in system.lt. -Running moltemplate.sh on system.lt (using "moltemplate.sh system.lt") -creates new LAMMPS data and input files: -system.data, system.in, system.in.init, system.in.settings -(These files are referenced in run.in.nvt.) - -You can run a simulation from the files created by moltemplate using - -lmp_linux -i run.in.nvt - -NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY - ALTERED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY WHEN SIMULATED. - (This was done to protect the original source of the files.) - The goal of this example is only to demonstrate how to use - "ltemplify.py" to convert lammps input and data files into - LT format and back again.) - - ----------- - -Instructions: -Execute the commands in: - -step 1) -README_run_ltemplify.sh - -and then - -step 2) -README_run_moltemplate.sh - -step 3) OPTIONAL - -To run a short LAMMPS simulation, you can use the "in.nvt" file, for example: - -$LAMMPS_BINARY -i run.in.nvt - -where "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). - ----------- diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh deleted file mode 100755 index 813c406c0e..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh +++ /dev/null @@ -1,16 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The "run.in.nvt" LAMMPS input script links to the input -# scripts and data files you hopefully have created earlier -# with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_run_moltemplate.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps this way: - -lmp_linux -i run.in.nvt - -# NOTE: BECAUSE ALL OF THE ORIGINAL FORCE FIELD PARAMETERS WERE INTENTIONALLY -# REMOVED, THE SYSTEM WILL MOVE IN A VERY UNREALISTIC WAY. diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh deleted file mode 100755 index 4bb42d7ea6..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/bin/sh - -# Aysun Itai's LAMMPS files contain two molecules: - -# The CNAD molecule has molecule-id 1 - -ltemplify.py -name CNAD -molid "1" cnad-cnt.in cnad-cnt.data > cnad.lt - -# The CNT (carbon nanotube) corresponds to molecule-id 2 -ltemplify.py -name CNT -molid "2" cnad-cnt.in cnad-cnt.data > cnt.lt - -# This will extract both molecules and save them as separate .LT files. -# (We can include these files later when preparing new simulations.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh deleted file mode 100755 index c99d4b9729..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh +++ /dev/null @@ -1,18 +0,0 @@ -# --- Running Moltemplate --- -# -- Prerequisites: -- -# The "system.lt" moltemplate file links to other ".lt" files -# files you hopefully have created earlier when you ran "ltemplify.py: -# cnad.lt and cnt.lt -# If not, carry out the instructions in "README_run_ltemplify.sh". - -moltemplate.sh system.lt - -# This will generate various files with names ending in *.in* and *.data. -# These files are the input files directly read by LAMMPS. - -# Optional: -# The "./output_ttree/" directory is full of temporary files generated by -# moltemplate. They can be useful for debugging, but are usually thrown away. - -rm -rf output_ttree/ - diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt deleted file mode 100644 index 3b9be3e9c3..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualize.txt +++ /dev/null @@ -1,50 +0,0 @@ - - ------- To view the trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - - -Later, to Load a trajectory in VMD: - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it - ------ Wrap the coordinates to the unit cell - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Enter: - - DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. - LOOKUP "pbctools" FOR DETAILS. - - pbc wrap -compound res -all - pbc box - -3) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data deleted file mode 100644 index 1f18ff4aef..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.data +++ /dev/null @@ -1,1157 +0,0 @@ -Created by Aysun Itai and modified by Andrew Jewett -NOTE: This file has been extensively modified. -Only the bond connectivity and atomic positions are accurate. - - 101 atoms - 134 bonds - 252 angles - 457 dihedrals - 0 impropers - - 16 atom types - 24 bond types - 50 angle types - 78 dihedral types - 0 improper types - - 0 50 xlo xhi - 0 50 ylo yhi - 0 50 zlo zhi - -Masses - - 1 10.0 - 2 10.0 # atom type names often appear - 3 10.0 # in the comments follwing - 4 10.0 # each line in the Masses section - 5 10.0 - 6 10.0 - 7 10.0 - 8 10.0 - 9 10.0 - 10 10.0 - 11 10.0 - 12 10.0 - 13 10.0 - 14 10.0 - 15 10.0 - 16 10.0 - -Atoms - -1 2 1 0.000000 12.345 10.000 4.328 -2 2 1 0.000000 12.031 11.173 5.037 -3 2 1 0.000000 12.031 11.173 6.455 -4 2 1 0.000000 11.173 12.031 7.164 -5 2 1 0.000000 11.173 12.031 4.328 -6 2 1 0.000000 10.000 12.345 5.037 -7 2 1 0.000000 10.000 12.345 6.455 -8 2 1 0.000000 8.827 12.031 7.164 -9 2 1 0.000000 8.827 12.031 4.328 -10 2 1 0.000000 7.969 11.173 5.037 -11 2 1 0.000000 7.969 11.173 6.455 -12 2 1 0.000000 7.655 10.000 7.164 -13 2 1 0.000000 7.655 10.000 4.328 -14 2 1 0.000000 7.969 8.827 5.037 -15 2 1 0.000000 7.969 8.827 6.455 -16 2 1 0.000000 8.827 7.969 7.164 -17 2 1 0.000000 8.827 7.969 4.328 -18 2 1 0.000000 10.000 7.655 5.037 -19 2 1 0.000000 10.000 7.655 6.455 -20 2 1 0.000000 11.173 7.969 7.164 -21 2 1 0.000000 11.173 7.969 4.328 -22 2 1 0.000000 12.031 8.827 5.037 -23 2 1 0.000000 12.031 8.827 6.455 -24 2 1 0.000000 12.345 10.000 7.164 -25 2 1 0.000000 12.345 10.000 8.582 -26 2 1 0.000000 12.031 11.173 9.291 -27 2 1 0.000000 12.031 11.173 10.709 -28 2 1 0.000000 11.173 12.031 11.418 -29 2 1 0.000000 11.173 12.031 8.582 -30 2 1 0.000000 10.000 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a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnad-cnt.in +++ /dev/null @@ -1,49 +0,0 @@ -#Created by Aysun Itai and modified by Andrew Jewett -# NOTE: This file has been extensively modified. -# Only the bond connectivity and atomic positions are accurate. - -units real - -neigh_modify delay 2 every 1 - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmm -pair_style lj/charmm/coul/charmm 8.0 10.0 -pair_modify mix arithmetic - -read_data cnad-cnt.data - -pair_coeff 1 1 0.02 4.0 -pair_coeff 2 2 0.02 1.0 # atoms will not interact sterically -pair_coeff 3 3 0.02 2.0 # in this version of the file. -pair_coeff 4 4 0.02 2.0 # (All pair forces and atom names removed) -pair_coeff 5 5 0.02 2.0 -pair_coeff 6 6 0.02 3.0 -pair_coeff 7 7 0.02 3.0 -pair_coeff 8 8 0.02 3.0 -pair_coeff 9 9 0.02 4.0 -pair_coeff 10 10 0.02 4.0 -pair_coeff 11 11 0.02 4.0 -pair_coeff 12 12 0.02 4.0 -pair_coeff 13 13 0.02 3.0 -pair_coeff 14 14 0.02 3.0 -pair_coeff 15 15 0.02 3.0 -pair_coeff 16 16 0.02 3.0 - -group cnt type 1 -group cnad type 2-16 - -displace_atoms cnad move 0 -7 0 units box -special_bonds charmm - -velocity all create 0.0 54321 dist uniform - -thermo 1 -thermo_style multi -timestep 0.005 - -dump 1 all atom 10 cnad-cnt.dump - -run 20000 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg deleted file mode 100644 index 3b79b405ef..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg deleted file mode 100644 index 1f46c1b7b2..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad-cnt_orig.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg deleted file mode 100644 index 628371b0d7..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnad.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg deleted file mode 100644 index 3489773adb..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/cnt.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf deleted file mode 100644 index 7b2b066767..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_after_rotate_and_copy.psf +++ /dev/null @@ -1,598 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 130 !NATOM - 1 1 1 1 0.000000 10.0000 0 - 2 1 1 1 0.000000 10.0000 0 - 3 1 1 1 0.000000 10.0000 0 - 4 1 1 1 0.000000 10.0000 0 - 5 1 1 1 0.000000 10.0000 0 - 6 1 1 1 0.000000 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diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf deleted file mode 100644 index cb8d7eda97..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/images/for_visualization/psf_file_created_by_topotools/cnad-cnt_orig.psf +++ /dev/null @@ -1,489 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 101 !NATOM - 1 2 1 1 0.000000 10.0000 0 - 2 2 1 1 0.000000 10.0000 0 - 3 2 1 1 0.000000 10.0000 0 - 4 2 1 1 0.000000 10.0000 0 - 5 2 1 1 0.000000 10.0000 0 - 6 2 1 1 0.000000 10.0000 0 - 7 2 1 1 0.000000 10.0000 0 - 8 2 1 1 0.000000 10.0000 0 - 9 2 1 1 0.000000 10.0000 0 - 10 2 1 1 0.000000 10.0000 0 - 11 2 1 1 0.000000 10.0000 0 - 12 2 1 1 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0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 0 0 0 - 0 0 0 0 0 - - 1 0 !NGRP - 0 0 0 - diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt deleted file mode 100644 index 5c1d2d4172..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/run.in.nvt +++ /dev/null @@ -1,46 +0,0 @@ -########################################################### -# Interaction of a carbon nanotube with a pair of mystery -# molecules (extracted from the cnat-cnt.data/in files). -########################################################### -# -# define the system being simulated: - -# -- init section -- -include system.in.init - -# -- atom definition section -- - -read_data system.data - -# -- settings section -- - -include system.in.settings - -# -- run section -- - - -timestep 0.05 -dump 1 all custom 2000 traj_nvt.lammpstrj id mol type x y z ix iy iz - -# The Nose-Hoover thermostat used with "fix nvt" can produce very odd-looking -# dynamics in dilute systems with few atoms (such as this one). -# Commenting this next line out: - -# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - -# Alternately, I receive fewer questions if I use langevin/nve instead: -fix fxlan all langevin 300.0 300.0 1000.0 48279 scale 3 1.5 -fix fxnve all nve - - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data -#thermo_modify flush yes - -#restart 1000000 restart_nvt - -run 500000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt deleted file mode 100644 index 70fdb7548b..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/system.lt +++ /dev/null @@ -1,29 +0,0 @@ -#Define the CNT and CNAD molecules, by including the files which define them -import cnt.lt -import cnad.lt - -# The cnt's center was originally at position 10,10,10, -# so I moved it back to the origin -cnt = new CNT.move(-10,-10,-10) - -# Rotation around the center of mass does not work (yet), -# so instead you have to move the molecule to the origin, -# rotate it, and move it back to where you want it. -# That's why the next line contains move().rot().move() -# I'll add center-of-mass rotation as a later feature. - -cnad1 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(90,0,1,0).move(-7,0,0) -cnad2 = new CNAD.move(0.611276,-0.0237931,-0.0487586).rot(-90,0,1,0).move(7,0,0) - - -# You can leave the periodic boundary conditions unspecified -# and change them later, OR you can declare them -# using the "write_once("Data Boundary") {}" command: - -write_once("Data Boundary") -{ - 0 50.0 xlo xhi - 0 50.0 ylo yhi - 0 50.0 zlo zhi -} - diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh deleted file mode 100755 index cf51fa8705..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # minimization and simulation at constant pressure - -# or - -lmp_linux -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -# or -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh deleted file mode 100755 index 3a08212692..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt deleted file mode 100644 index 73358e55dc..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 500 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg b/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg deleted file mode 100644 index 2cdc08b312..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/ice_crystal/images/ice_rect8_crystal_3x2x2_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt deleted file mode 100644 index 2b550b6309..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt deleted file mode 100644 index ccfd2f18c6..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/spce_ice_rect8.lt +++ /dev/null @@ -1,57 +0,0 @@ -# This ice (1h) unit cell is rectangular and contains 8 water molecules. -# (Coordinates and cell dimensions converted were from a PDB file.) -# The dimensions of the unit cell (in Angstroms) are: 4.521 7.832 7.362 - - -import "spce.lt" # <-- define the "SPCE" molecule - -SpceIceRect8 { - - # Create a 3-dimensional array of 8 water molecules - - wat = new SPCE[2][2][2] - - # Array indices will be correlated with position [xindex][yindex][zindex] - - # You can overwrite coordinates of atoms after they were created this way: - # (Order is not important) - # atom-ID molecule-ID atomType charge newX newY newZ - - write("Data Atoms") { - $atom:wat[1][0][0]/O $mol:wat[1][0][0] @atom:SPCE/O -0.8476 3.391 1.305 1.381 - $atom:wat[1][0][0]/H1 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 3.391 0.370 1.710 - $atom:wat[1][0][0]/H2 $mol:wat[1][0][0] @atom:SPCE/H 0.4238 2.582 1.772 1.710 - $atom:wat[1][0][1]/O $mol:wat[1][0][1] @atom:SPCE/O -0.8476 3.391 1.305 5.981 - $atom:wat[1][0][1]/H1 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 3.391 1.305 6.970 - $atom:wat[1][0][1]/H2 $mol:wat[1][0][1] @atom:SPCE/H 0.4238 4.200 1.772 5.652 - $atom:wat[0][0][0]/O $mol:wat[0][0][0] @atom:SPCE/O -0.8476 1.131 2.611 2.300 - $atom:wat[0][0][0]/H1 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 1.131 2.611 3.289 - $atom:wat[0][0][0]/H2 $mol:wat[0][0][0] @atom:SPCE/H 0.4238 0.320 2.143 1.971 - $atom:wat[0][0][1]/O $mol:wat[0][0][1] @atom:SPCE/O -0.8476 1.131 2.611 5.061 - $atom:wat[0][0][1]/H1 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.940 2.143 5.391 - $atom:wat[0][0][1]/H2 $mol:wat[0][0][1] @atom:SPCE/H 0.4238 1.131 3.546 5.391 - $atom:wat[0][1][0]/O $mol:wat[0][1][0] @atom:SPCE/O -0.8476 1.131 5.221 1.381 - $atom:wat[0][1][0]/H1 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 1.131 4.286 1.710 - $atom:wat[0][1][0]/H2 $mol:wat[0][1][0] @atom:SPCE/H 0.4238 0.320 5.688 1.710 - $atom:wat[0][1][1]/O $mol:wat[0][1][1] @atom:SPCE/O -0.8476 1.131 5.221 5.981 - $atom:wat[0][1][1]/H1 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.131 5.221 6.970 - $atom:wat[0][1][1]/H2 $mol:wat[0][1][1] @atom:SPCE/H 0.4238 1.940 5.688 5.652 - $atom:wat[1][1][0]/O $mol:wat[1][1][0] @atom:SPCE/O -0.8476 3.391 6.526 2.300 - $atom:wat[1][1][0]/H1 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 3.391 6.526 3.289 - $atom:wat[1][1][0]/H2 $mol:wat[1][1][0] @atom:SPCE/H 0.4238 2.582 6.058 1.971 - $atom:wat[1][1][1]/O $mol:wat[1][1][1] @atom:SPCE/O -0.8476 3.391 6.526 5.061 - $atom:wat[1][1][1]/H1 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 4.200 6.058 5.391 - $atom:wat[1][1][1]/H2 $mol:wat[1][1][1] @atom:SPCE/H 0.4238 3.391 7.462 5.391 - } -} # IceRect8 - -# Credit goes to Martin Chaplin. -# These coordinates were orignally downloaded from Martin Chaplin's -# website: http://www.btinternet.com/~martin.chaplin/ice1h.html -# ... and then they were stretched independently in the xy and z -# directions in order to match the lattice parameters measured by -# Rottger et al., -# "Lattice constants and thermal expansion of H2O and D2O ice Ih" -# between 10 and 265K", Acta Crystallogr. B, 50 (1994) 644-648 -# I am using the lattice constants measured at temperature 265K -# (and pressure=100Torr). diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt deleted file mode 100644 index b4f22f9dcf..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/moltemplate_files/system.lt +++ /dev/null @@ -1,11 +0,0 @@ -import "spce_ice_rect8.lt" - -cells = new SpceIceRect8 [3].move(4.521, 0.0, 0.0) - [2].move( 0.0, 7.832, 0.0) - [2].move( 0.0, 0.0, 7.362) - -write_once("Data Boundary") { - 0 13.563 xlo xhi - 0 15.664 ylo yhi - 0 14.724 zlo zhi -} diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt deleted file mode 100644 index 2bf2e0c03f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.npt +++ /dev/null @@ -1,38 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 2.0 -dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 400.0 400.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - -thermo 100 -#thermo_modify flush yes - -run 20000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt deleted file mode 100644 index b23a288c47..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/ice_crystal/run.in.nvt +++ /dev/null @@ -1,61 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Until then, try "read_dump", "dump2data.py", or "restart2data". - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - - -timestep 2.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - - -thermo 500 -#thermo_modify flush yes - - -#restart 100000 restart_nvt - -run 50000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT deleted file mode 100644 index 83b4ad80bf..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README.TXT +++ /dev/null @@ -1,51 +0,0 @@ -This is a small version of a carbon-nanotube, water capillary system. -It was inspired by this paper: - - Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) - --------- Requirements: ------- -To run this system at constant pressure, it might help to compile LAMMPS -with the optional RIGID package, and use "fix rigid" on the carbon. -(The use of fix rigid is controversial.) Running at NVT does not require this. ------------------------------- - -Note: To investigate the behavior from that paper, it might be a good - idea to increase the size of the water reservoir, the spacing between - the walls, and the size of the system in the X and Y directions. - -Note: Explicit carbon-carbon bonds: - In the graphene and nanotube structures, I did not try to connect the - carbon atoms together with bonds. Instead we will hold these structures - rigid by not integrating their equations of motion. - (If you want to simulate movement of the carbon atoms at high - temperatures or tension, LAMMPS has 3-body/many-body LAMMPS force-fields - available for simulating the behaviour of carbon in graphite. I know - that you don't need to specify bonds to use these force fields. I do - not know know if these force fields work for nanotubes or graphene.) - -Note: Other modeling tools: - If you need explicit bonds between carbon atoms, then you must add them - yourself or use a different tool. Currently (2012-10-20), moltemplate does - not generate bonds automatically. The "Nanotube Builder" and "topotools" - plugins for for VMD can generate a nanotube with bonds in LAMMPS data - format. You can then convert this data file to .LT format using the - ltemplify.py utility and then import it into another .LT file and play - with it later. (In the "cnad-cnt" example, the carbon nanotube was built - using "Nanotube Builder" and topotools, and processed with ltemplify.py) - - -# WARNING: THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. -# A real junction would be curved and deformed near the boundary, -# (not 90 degrees) and it would not be built entirely from hexagons. -# (This is not a problem in this example because the carbon atoms -# are immobilized.) If you want to simulate the behavior of -# real graphene or nanotube junctions, you must be more careful. -# To solve this problem: -# Moltemplate allows you to move, customize or delete individual -# atoms near the boundary. You can move atoms by overwriting their -# coordinates using additional write("Data Atoms") statements (after -# the walls and tube are created). You can also change their charge. -# Alternately, you could start with the structure provided here, and -# relax/minimize the coordinates of the carbon atoms using LAMMPS -# before using it in other simulations. -# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh deleted file mode 100755 index 8a470b9551..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_run.sh +++ /dev/null @@ -1,24 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.nvt # minimization and simulation at constant volume -lmp_linux -i run.in.npt # minimization and simulation at constant pressure - # (WARNING: The "run.in.npt" example has not been - # rigorously tested and may fail.) - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt deleted file mode 100644 index 206db99038..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/README_visualize.txt +++ /dev/null @@ -1,77 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - To shift the box by a fraction in the x direction (for example) - do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } - pbc box -shiftcenterrel {-0.50 -0.52 0.0 } - - # Alternately if you have a solute whose atoms are all of type 1, - # then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index bf019b4c31..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,3195 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD-generated NAMD/X-Plor PSF structure file - - 2454 !NATOM - 1 1 1 1 0.000000 12.0000 0 - 2 1 1 1 0.000000 12.0000 0 - 3 2 1 1 0.000000 12.0000 0 - 4 2 1 1 0.000000 12.0000 0 - 5 3 1 1 0.000000 12.0000 0 - 6 3 1 1 0.000000 12.0000 0 - 7 4 1 1 0.000000 12.0000 0 - 8 4 1 1 0.000000 12.0000 0 - 9 5 1 1 0.000000 12.0000 0 - 10 5 1 1 0.000000 12.0000 0 - 11 6 1 1 0.000000 12.0000 0 - 12 6 1 1 0.000000 12.0000 0 - 13 7 1 1 0.000000 12.0000 0 - 14 7 1 1 0.000000 12.0000 0 - 15 8 1 1 0.000000 12.0000 0 - 16 8 1 1 0.000000 12.0000 0 - 17 9 1 1 0.000000 12.0000 0 - 18 9 1 1 0.000000 12.0000 0 - 19 10 1 1 0.000000 12.0000 0 - 20 10 1 1 0.000000 12.0000 0 - 21 11 1 1 0.000000 12.0000 0 - 22 11 1 1 0.000000 12.0000 0 - 23 12 1 1 0.000000 12.0000 0 - 24 12 1 1 0.000000 12.0000 0 - 25 13 1 1 0.000000 12.0000 0 - 26 13 1 1 0.000000 12.0000 0 - 27 14 1 1 0.000000 12.0000 0 - 28 14 1 1 0.000000 12.0000 0 - 29 15 1 1 0.000000 12.0000 0 - 30 15 1 1 0.000000 12.0000 0 - 31 16 1 1 0.000000 12.0000 0 - 32 16 1 1 0.000000 12.0000 0 - 33 17 1 1 0.000000 12.0000 0 - 34 17 1 1 0.000000 12.0000 0 - 35 18 1 1 0.000000 12.0000 0 - 36 18 1 1 0.000000 12.0000 0 - 37 19 1 1 0.000000 12.0000 0 - 38 19 1 1 0.000000 12.0000 0 - 39 20 1 1 0.000000 12.0000 0 - 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Chem. Phys. 135(21):214705 (2011) -# -# Note: To investigate the behavior from that paper, you would have to increase -# the spacing between the two graphene sheets to prevent the water from -# making contact with the lower graphene wall. -# -# Requirements: 1) Set your $MOLTEMPLATE_PATH variable -# 2) The "RIGID" LAMMPS package may be needed later -# To run this system at constant pressure, it might help to compile LAMMPS with -# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) -# -# Also, if you have not yet done this set your MOLTEMPLATE_PATH environment -# variable to access it. (See installation instructions.) -# Most likely some of the files in this example (like graphene.lt, tip3p2004.lt) -# are not in this directory, but are in the "common" directory. -# Set MOLTEMPLATE_PATH to point to the "common" directory. -# -# ----------------------------------------------------------- -# -# To run moltemplate, use: - -moltemplate.sh system.lt - -# This will generate:system.data, system.in, system.in.init, system.in.settings diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt deleted file mode 100644 index 9122dc1376..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene.lt +++ /dev/null @@ -1,107 +0,0 @@ -# This file contains a unit cell for building graphene and nanotubes -# -# -# The 2AtomCellAlignX "molecule" defined below is a minimal unit cell for any -# hexagonal tesselation in 2-dimensions. (See "graphene_unit_cell.jpg") -# Surfaces constructed with this unit cell can be flat or curved into tubes. -# The distance between nearest-neighbor carbon atoms (ie the length of a -# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. -# -# d = length of each hexagon's side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms -# w = width of hexagon rows = 1.5*l = 2.13 Angstroms -# -# Consequently, the Lattice-cell vectors for singe-layer graphene are: -# (2.4595121467478, 0, 0) (aligned with X axis) -# (1.2297560733739, 2.13, 0) (2.13 = 1.5*d) -# So, to build a sheet of graphite, you could use: -# sheet = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) - - - - -Graphene { - - 2AtomCellAlignX - { - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 - $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 - } - } - - # Now define properties of the Carbon graphene atom - - write_once("In Init") { - pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 - } - - write_once("Data Masses") { - @atom:C 12.0 - } - - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/charmm/coul/charmm 0.068443 3.407 - - # These Lennard-Jones parameters come from - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - - # Define a group consisting of only carbon atoms in graphene molecules - group Cgraphene type @atom:C - } - - # Notice that the two atoms in the unit-cell above lie in the XY plane. - # (Their z-coordinate is zero). It's also useful to have a version of - # this object which lies in the XZ plan. So we define this below: - - 2AtomCellAlignXZ = 2AtomCellAlignX.rot(90,1,0,0) - -} # Graphene - - - - - - - - - - -# ------------ Graphite ----------- -# -# Note: For graphite: sheets stacked in the Z direction are separated by a -# distance of 3.35 Angstroms, and shifted in an alternating +/-Y direction -# by a distance of d (1.42 Angstroms). To add additional graphene layers -# you could use: -# sheet2 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet2[*][*].move(0, 1.42, 3.35) -# sheet3 = new Graphene/2AtomCellAlignX [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# sheet3[*][*].move(0, -1.42, 6.70) -# etc... -# However, to build a thick sheet of graphite, it would -# be more efficient to use a 4-atom unit cell: -# -#Graphene { -# GraphiteCell { -# # atomID molID atomType charge x y z -# write("Data Atoms") { -# $atom:C1 $mol:... @atom:../C 0.0 -0.61487803668695 -0.355 0.0 -# $atom:C2 $mol:... @atom:../C 0.0 0.61487803668695 0.355 0.0 -# $atom:C3 $mol:... @atom:../C 0.0 -0.61487803668695 1.065 3.35 -# $atom:C4 $mol:... @atom:../C 0.0 0.61487803668695 1.775 3.35 -# } -# } # GraphiteCell -#} -# -# Then you could create a thick sheet of graphite this way: -# -# graphite = new Graphene/GraphiteCell [10].move(2.4595121467478,0,0) -# [10].move(1.2297560733739,2.13,0) -# [5].move(0,0,6.70) diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt deleted file mode 100644 index 53499334de..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/graphene_walls.lt +++ /dev/null @@ -1,54 +0,0 @@ - -import "graphene.lt" - -# -------------- graphene sheet ----------------- - -# Notes: -# Hexagonal lattice with: -# d = length of each hexagonal side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478 Angstroms -# w = width of hexagon rows = 1.5*d = 2.13 Angstroms - -Wall { - unitcells = new Graphene/2AtomCellAlignX [14].move(1.2297560733739, 2.13, 0) - [13].move(2.4595121467478, 0, 0) - unitcells[*][*].move(-24.595121467478, -14.91, 0.000) - - # Now cut a hole in the graphene sheet roughly where the nanotube is located - delete unitcells[5][7-8] # delete 2 unit cells (2 atoms each, 4 atoms total) - delete unitcells[6][6-8] # delete 3 unit cells (2 atoms each, 6 atoms total) - delete unitcells[7][5-8] # delete 4 unit cells (2 atoms each, 8 atoms total) - delete unitcells[8][5-7] # delete 3 unit cells (2 atoms each, 6 atoms total) - delete unitcells[9][5-6] # delete 2 unit cells (2 atoms each, 4 atoms total) - # Optional fine tuning: delete a few additional atoms around the edges - delete unitcells[5][6]/C2 # delete a single atom - delete unitcells[6][5]/C2 # delete a single atom - delete unitcells[6][9]/C1 # delete a single atom - delete unitcells[8][4]/C2 # delete a single atom - delete unitcells[8][8]/C1 # delete a single atom - delete unitcells[9][7]/C1 # delete a single atom -} - -# Make two copies of the wall, and place them on either end of the nanotube - -wall1 = new Wall.move(0, 0, 32.0) -wall2 = new Wall.move(0, 0, 58.26) - - -# WARNING: A reader has emailed me to point out that: -# THIS IS NOT A REALISTIC MODEL OF A GRAPHENE-NANOTUBE JUNCTION. -# A real junction would be curved and deformed near the boundary, -# (not 90 degrees) and it would not be built entirely from hexagons. -# (This is not a problem in this example because the carbon atoms -# are immobilized.) If you want to simulate the behavior of -# real graphene or nanotube junctions, you must be more careful. -# To solve this problem: -# Moltemplate allows you to move, customize or delete individual -# atoms near the boundary. You can move atoms by overwriting their -# coordinates using additional write("Data Atoms") statements (after -# the walls and tube are created). You can also change their charge. -# Alternately, you could start with the structure provided here, and -# relax/minimize the coordinates of the carbon atoms using LAMMPS -# before using it in other simulations. -# Or you could do both (customization & minimization). diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt deleted file mode 100644 index 02d7dd762d..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt +++ /dev/null @@ -1,24 +0,0 @@ -import "graphene.lt" - -# ------------------ nanotube --------------- - -# Now use this to build a simple ("zigzag") nanotube where the long-axis of each -# hexagon is aligned with the tube axis (along the Z direction). If the -# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of -# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon -# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms -# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms. - - -nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R - [14].rot(25.7142857,0,0,1) #25.7=360/14 - [12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14 - #2.13= d*1.5 - - # Note: The length is 12 hexegons, the circumference is - # 14 hexegons (~=25.56 and 34.43 Angstroms, respectively). - -# Move all of the unit-cells in the nanotube between the two graphene sheets. - -nanotube[*][*].move(0, 0, 33.42) - diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt deleted file mode 100644 index 3bb7bca40a..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 200.0 1.0 - angle_coeff @angle:HOH harmonic 200.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt deleted file mode 100644 index d46057fafd..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/system.lt +++ /dev/null @@ -1,38 +0,0 @@ -# This is a small version of a carbon-nanotube, water capillary system. It was -# inspired by this paper: Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) - -import "graphene_walls.lt" - -import "nanotube.lt" - -import "water_box.lt" - - -# ------------ boundary conditions ------------ - -write_once("Data Boundary") { - -15.98682895386 15.98682895386 xlo xhi - -14.91 14.91 ylo yhi - 0.0 80.00 zlo zhi -} - -# --------------------------------------------- - - - -write_once("In Init") { - # -- override any earlier pair_style settings: -- - pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5 & - lj/charmm/coul/charmm 9.0 10.0 -} - - -write_once("In Settings") { - # --- We must eventually specify the interactions between the atoms --- - # --- in different molecule types (graphene-water interactions). --- - # (See Laurent Joly, J. Chem. Phys. 135(21):214705 (2011) for details - - pair_coeff @atom:Graphene/C @atom:SPCE/O lj/charmm/coul/long 0.114 3.28 - pair_coeff @atom:Graphene/C @atom:SPCE/H lj/charmm/coul/long 0.0 3.28 -} - diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt deleted file mode 100644 index c825276f5a..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/water_box.lt +++ /dev/null @@ -1,20 +0,0 @@ -import "spce.lt" - -# --------------- water ------------------ - -# Create a rhombohedral box of water. (A rectangular box works also.) - -wat = new SPCE [9].move(3.5526287, 0, 0 ) - [9].move(1.77631435, 3.3133, 0 ) - [6].move( 0, 0, 3.45) - -# Optional: Center the water box at the origin. (Not really necessary.) - -wat[*][*][*].move(-23.9802437, -14.90985, 11.47) - -# --------------- Note: ----------------- -# The spacing between water molecules does not matter much as long as it is -# reasonable. (I adjusted the spacing try to insure that the waters are spread -# uniformly throughout the box. We do not want bubles to form if there are -# gaps near the XY periodic boundaries.) We will have to equilibrate it later. - diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt deleted file mode 100644 index 608b4fa382..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt +++ /dev/null @@ -1,98 +0,0 @@ -# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED. -# (This simulation may fail. -# However the "run.in.nvt" example in this directory should work.) -# -# Requirements: -# To run this system at constant pressure, it might help to compile LAMMPS with -# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.) -# The use of fix rigid is controversial. This method is demonstrated below. - -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# Only the Cgraphene atoms are immobile. -group mobile subtract all Cgraphene - - -# Unfortunately you can not use the LAMMPS "minimize" command on this system -# because there is no way to immobilize the carbon graphene & nanotube atoms -# during minimization. Instead, we can use langevin dynamics with a large -# damping parameter and a small timestep. - -print "--------- beginning minimization (using fix langevin) ---------" - -timestep 0.1 -fix fxlan mobile langevin 1.0 1.0 100.0 48279 -fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) -thermo 100 -run 2500 - -unfix fxlan -unfix fxnve - -# -- simulation protocol -- - -print "--------- beginning simulation (using fix nvt) ---------" - -timestep 0.5 -dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 1000 # time interval for printing out "thermo" data - - - - - -# ------------------------- NPT --------------------------- - -# Set temp=300K, pressure=100bar, and equilibrate volume only in the z direction - -fix fxMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile - -# ------ CONTROVERSIAL (see below): ------ - -fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 100 100 1000.0 force * off off off torque * off off off dilate mobile - -# -- Alternate npt rigid method -- -# I'm not sure which way is more correct, however -# this also seems to behave in a reasonable-looking way: -#fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off -# -# The use of either "fix rigid" or "fix rigid/npt" to immobilize -# an object is somewhat controversial. Feel free to omit it. -#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing -#molecules, but I noticed that at NPT, it does a better job of maintaining -# the correct volume. However "fix rigid" has changed since then (2011), -# so this may no longer be true. Please use this example with caution.) -# ---------------------------------------- - -# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the -# forces between immobilized atoms. -neigh_modify exclude group Cgraphene Cgraphene - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp -compute pressMobile all pressure tempMobile - -thermo_style custom step c_tempMobile c_pressMobile temp press vol - -fix_modify fxMoveStuff temp tempMobile - -run 100000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt deleted file mode 100644 index f4fd0bbc15..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt +++ /dev/null @@ -1,71 +0,0 @@ -# ----------------------------- Initialization Section -------------------- - -include system.in.init - - -# ----------------------------- Atom Definition Section ------------------- - -read_data system.data - - -# ----------------------------- Settings Section -------------------------- - -include system.in.settings - - -# ----------------------------- Run Section ------------------------------- - - - -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms. (Note: This is not optional under NPT conditions.) -neigh_modify exclude group Cgraphene Cgraphene - -# Only the Cgraphene atoms are immobile. -group mobile subtract all Cgraphene - - - -# -- minimization protocol -- - -# Unfortunately you can not use the LAMMPS "minimize" command on this system -# because there is no way to immobilize the carbon graphene & nanotube atoms -# during minimization. Instead, we can use langevin dynamics with a large -# damping parameter and a small timestep. - -print "--------- beginning minimization (using fix langevin) ---------" - -timestep 0.1 -fix fxlan mobile langevin 1.0 1.0 100.0 48279 -fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation) -thermo 100 -run 2500 - -unfix fxlan -unfix fxnve - -# -- simulation protocol -- - -print "--------- beginning simulation (using fix nvt) ---------" - -timestep 1.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed -thermo 500 # time interval for printing out "thermo" data - - -# Integrate the equations of motion: -fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0 - -# The next two lines recalculate the temperature -# using only the mobile degrees of freedom: - -compute tempMobile mobile temp -fix_modify fxMoveStuff temp tempMobile - -restart 5000000 restart_nvt -run 10000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT deleted file mode 100644 index 0e58ef44c7..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README.TXT +++ /dev/null @@ -1,10 +0,0 @@ -This is a simple system of 260 water molecules. - -In this example, the coordinates of the atoms are read from a PDB file -instead of being specified manually (as well as the boundary information). - -The PDB file was generated by the useful "solvate" utility which comes with VMD. -(To generate this file yourself, run VMD, click on the "Extensions" menu, -and select Modeling-->Add Solvation Box. -In this example, I made a box whose x,y,z dimensions were 16,24,24.) - diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh deleted file mode 100755 index 022c53ce3b..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # minimization and simulation at constant pressure -lmp_linux -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh deleted file mode 100755 index 5d2be21331..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_setup.sh +++ /dev/null @@ -1,32 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - -cd moltemplate_files/ # (The .lt input files are in this directory) - - moltemplate.sh -pdb solvate.pdb system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ - - -# -#This will prepare LAMMPS input files for a box of water -#(In this example, we are using the "SPC/E" water model.) -#The number of water molecules in the "wat = new SPCE [260]" command -#must equal the number of water molecules in the PDB file. -# -#Coordinates and boundary-box information is read from the .pdb file. -# -#You can also specify this information directly in the ttree file. -#See the comments section in "system.lt" for details. -# diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt deleted file mode 100644 index 8063d535f8..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/README_visualize.txt +++ /dev/null @@ -1,64 +0,0 @@ - ------- Instructions to view a trajectory in VMD -------- - - ------- Disclaimer ------- - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - - (Note, at this point the image shown in the VMD graphics window may - not appear correct or incomplete. The coordinates of the atoms may - overlap if you asked moltemplate.sh to load your coordinates from - a PDB or XYZ file. - However, later after you have run a simulation, the trajectories - should appear reasonably correct when you load them in VMD using - the PSF file you just generated.) - - -Later, to Load a trajectory in VMD: - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it - ------ Wrap the coordinates to the unit cell - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Enter: - - DISCLAIMER: I'M NOT SURE THESE COMMANDS ARE CORRECT. - LOOKUP "pbctools" FOR DETAILS. - - pbc wrap -compound res -all - pbc box - - # If you have a solute of type 1, then use this: - #pbc wrap -sel type=1 -all -centersel type=2 -center com - -"1" corresponds to the "O" atom type -"2" corresponds to the "H" atom type - -3) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types: - -sed -e 's/ 1 1 / O O /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > system.psf - -(If you do this, I guess that you might have to use - "type=O" and "type=H" in step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh deleted file mode 100755 index 4ebc7b17a3..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/README.sh +++ /dev/null @@ -1,11 +0,0 @@ - -# Run moltemplate this way: - -moltemplate.sh -pdb solvate.pdb system.lt - - -# The PDB file was generated by the "solvate" utility which comes with VMD. -# (To generate this file yourself, run VMD, click on the "Extensions" menu, -# and select Modeling-->Add Solvation Box. -# In this example, I made a box whose x,y,z dimensions were 16,24,24.) - diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb deleted file mode 100644 index 0ed5103cbb..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb +++ /dev/null @@ -1,782 +0,0 @@ -CRYST1 16.000 24.000 24.000 90.00 90.00 90.00 P 1 1 -ATOM 1 OH2 TIP3W 5 3.668 10.082 15.904 1.00 0.00 WT1 O -ATOM 2 H1 TIP3W 5 3.224 10.451 15.101 1.00 0.00 WT1 H -ATOM 3 H2 TIP3W 5 3.092 10.379 16.627 1.00 0.00 WT1 H -ATOM 4 OH2 TIP3W 7 6.033 4.876 20.891 1.00 0.00 WT1 O -ATOM 5 H1 TIP3W 7 6.078 5.224 21.798 1.00 0.00 WT1 H -ATOM 6 H2 TIP3W 7 6.592 4.088 20.961 1.00 0.00 WT1 H -ATOM 7 OH2 TIP3W 21 5.186 16.696 12.072 1.00 0.00 WT1 O -ATOM 8 H1 TIP3W 21 6.083 16.979 11.816 1.00 0.00 WT1 H -ATOM 9 H2 TIP3W 21 5.337 15.832 12.490 1.00 0.00 WT1 H -ATOM 10 OH2 TIP3W 29 8.324 13.811 21.332 1.00 0.00 WT1 O -ATOM 11 H1 TIP3W 29 8.633 13.348 22.112 1.00 0.00 WT1 H -ATOM 12 H2 TIP3W 29 8.506 13.116 20.645 1.00 0.00 WT1 H -ATOM 13 OH2 TIP3W 44 3.786 16.318 1.310 1.00 0.00 WT1 O -ATOM 14 H1 TIP3W 44 3.781 15.388 1.196 1.00 0.00 WT1 H -ATOM 15 H2 TIP3W 44 4.528 16.580 0.781 1.00 0.00 WT1 H -ATOM 16 OH2 TIP3W 46 6.205 6.991 18.442 1.00 0.00 WT1 O -ATOM 17 H1 TIP3W 46 6.782 7.347 19.152 1.00 0.00 WT1 H -ATOM 18 H2 TIP3W 46 5.309 7.062 18.800 1.00 0.00 WT1 H -ATOM 19 OH2 TIP3W 48 2.750 8.844 9.629 1.00 0.00 WT1 O -ATOM 20 H1 TIP3W 48 2.110 8.290 9.998 1.00 0.00 WT1 H -ATOM 21 H2 TIP3W 48 2.164 9.245 8.962 1.00 0.00 WT1 H -ATOM 22 OH2 TIP3W 52 3.935 16.195 22.109 1.00 0.00 WT1 O -ATOM 23 H1 TIP3W 52 4.870 16.034 21.985 1.00 0.00 WT1 H -ATOM 24 H2 TIP3W 52 3.655 15.367 22.581 1.00 0.00 WT1 H -ATOM 25 OH2 TIP3W 64 10.674 8.909 4.986 1.00 0.00 WT1 O -ATOM 26 H1 TIP3W 64 10.998 8.871 5.932 1.00 0.00 WT1 H -ATOM 27 H2 TIP3W 64 9.748 9.270 5.075 1.00 0.00 WT1 H -ATOM 28 OH2 TIP3W 67 0.002 5.667 14.591 1.00 0.00 WT1 O -ATOM 29 H1 TIP3W 67 0.483 5.990 13.830 1.00 0.00 WT1 H -ATOM 30 H2 TIP3W 67 0.608 5.781 15.347 1.00 0.00 WT1 H -ATOM 31 OH2 TIP3W 68 9.882 9.156 14.916 1.00 0.00 WT1 O -ATOM 32 H1 TIP3W 68 9.574 9.753 15.597 1.00 0.00 WT1 H -ATOM 33 H2 TIP3W 68 10.021 8.264 15.289 1.00 0.00 WT1 H -ATOM 34 OH2 TIP3W 87 1.661 6.681 1.943 1.00 0.00 WT1 O -ATOM 35 H1 TIP3W 87 1.943 5.739 1.981 1.00 0.00 WT1 H -ATOM 36 H2 TIP3W 87 0.778 6.599 1.483 1.00 0.00 WT1 H -ATOM 37 OH2 TIP3W 88 4.821 20.603 11.239 1.00 0.00 WT1 O -ATOM 38 H1 TIP3W 88 5.466 20.782 11.963 1.00 0.00 WT1 H -ATOM 39 H2 TIP3W 88 5.384 20.914 10.456 1.00 0.00 WT1 H -ATOM 40 OH2 TIP3W 90 15.022 20.855 12.831 1.00 0.00 WT1 O -ATOM 41 H1 TIP3W 90 14.222 20.809 13.292 1.00 0.00 WT1 H -ATOM 42 H2 TIP3W 90 14.673 21.057 11.918 1.00 0.00 WT1 H -ATOM 43 OH2 TIP3W 94 1.339 3.782 22.814 1.00 0.00 WT1 O -ATOM 44 H1 TIP3W 94 0.839 3.425 22.087 1.00 0.00 WT1 H -ATOM 45 H2 TIP3W 94 1.775 3.077 23.138 1.00 0.00 WT1 H -ATOM 46 OH2 TIP3W 95 0.485 15.137 22.476 1.00 0.00 WT1 O -ATOM 47 H1 TIP3W 95 0.644 15.425 23.349 1.00 0.00 WT1 H -ATOM 48 H2 TIP3W 95 0.312 15.961 21.975 1.00 0.00 WT1 H -ATOM 49 OH2 TIP3W 111 10.426 7.604 2.404 1.00 0.00 WT1 O -ATOM 50 H1 TIP3W 111 10.761 8.401 1.994 1.00 0.00 WT1 H -ATOM 51 H2 TIP3W 111 10.248 7.889 3.308 1.00 0.00 WT1 H -ATOM 52 OH2 TIP3W 113 4.269 22.752 16.265 1.00 0.00 WT1 O -ATOM 53 H1 TIP3W 113 4.149 23.680 15.888 1.00 0.00 WT1 H -ATOM 54 H2 TIP3W 113 5.061 22.796 16.776 1.00 0.00 WT1 H -ATOM 55 OH2 TIP3W 130 10.926 5.365 1.018 1.00 0.00 WT1 O -ATOM 56 H1 TIP3W 130 11.138 4.769 1.754 1.00 0.00 WT1 H -ATOM 57 H2 TIP3W 130 10.657 6.212 1.493 1.00 0.00 WT1 H -ATOM 58 OH2 TIP3W 133 8.647 4.314 19.278 1.00 0.00 WT1 O -ATOM 59 H1 TIP3W 133 7.964 3.611 19.326 1.00 0.00 WT1 H -ATOM 60 H2 TIP3W 133 8.043 5.064 19.153 1.00 0.00 WT1 H -ATOM 61 OH2 TIP3W 134 8.381 17.319 23.275 1.00 0.00 WT1 O -ATOM 62 H1 TIP3W 134 7.516 17.340 23.695 1.00 0.00 WT1 H -ATOM 63 H2 TIP3W 134 8.431 18.263 23.009 1.00 0.00 WT1 H -ATOM 64 OH2 TIP3W 150 4.299 17.774 7.169 1.00 0.00 WT1 O -ATOM 65 H1 TIP3W 150 3.303 17.803 7.322 1.00 0.00 WT1 H -ATOM 66 H2 TIP3W 150 4.533 18.755 6.924 1.00 0.00 WT1 H -ATOM 67 OH2 TIP3W 152 8.892 12.977 5.321 1.00 0.00 WT1 O -ATOM 68 H1 TIP3W 152 8.119 12.478 5.443 1.00 0.00 WT1 H -ATOM 69 H2 TIP3W 152 9.342 12.557 4.536 1.00 0.00 WT1 H -ATOM 70 OH2 TIP3W 167 2.174 18.468 2.212 1.00 0.00 WT1 O -ATOM 71 H1 TIP3W 167 2.632 17.628 2.203 1.00 0.00 WT1 H -ATOM 72 H2 TIP3W 167 2.931 19.120 2.281 1.00 0.00 WT1 H -ATOM 73 OH2 TIP3W 239 13.612 17.680 18.622 1.00 0.00 WT1 O -ATOM 74 H1 TIP3W 239 13.744 17.414 19.508 1.00 0.00 WT1 H -ATOM 75 H2 TIP3W 239 14.526 17.831 18.347 1.00 0.00 WT1 H -ATOM 76 OH2 TIP3W 443 9.935 12.876 10.191 1.00 0.00 WT1 O -ATOM 77 H1 TIP3W 443 9.709 12.098 9.634 1.00 0.00 WT1 H -ATOM 78 H2 TIP3W 443 9.472 12.766 11.018 1.00 0.00 WT1 H -ATOM 79 OH2 TIP3W 450 7.060 2.074 19.830 1.00 0.00 WT1 O -ATOM 80 H1 TIP3W 450 7.650 1.619 20.528 1.00 0.00 WT1 H -ATOM 81 H2 TIP3W 450 6.148 1.796 20.035 1.00 0.00 WT1 H -ATOM 82 OH2 TIP3W 465 13.891 1.919 2.992 1.00 0.00 WT1 O -ATOM 83 H1 TIP3W 465 14.198 2.681 3.422 1.00 0.00 WT1 H -ATOM 84 H2 TIP3W 465 13.212 1.577 3.578 1.00 0.00 WT1 H -ATOM 85 OH2 TIP3W 466 8.823 10.581 8.827 1.00 0.00 WT1 O -ATOM 86 H1 TIP3W 466 8.183 10.753 8.148 1.00 0.00 WT1 H -ATOM 87 H2 TIP3W 466 8.389 10.061 9.534 1.00 0.00 WT1 H -ATOM 88 OH2 TIP3W 469 9.078 11.967 12.734 1.00 0.00 WT1 O -ATOM 89 H1 TIP3W 469 8.228 11.561 12.993 1.00 0.00 WT1 H -ATOM 90 H2 TIP3W 469 9.512 12.194 13.560 1.00 0.00 WT1 H -ATOM 91 OH2 TIP3W 484 10.282 0.640 2.053 1.00 0.00 WT1 O -ATOM 92 H1 TIP3W 484 10.367 0.959 3.016 1.00 0.00 WT1 H -ATOM 93 H2 TIP3W 484 9.743 1.323 1.667 1.00 0.00 WT1 H -ATOM 94 OH2 TIP3W 485 4.618 8.125 7.777 1.00 0.00 WT1 O -ATOM 95 H1 TIP3W 485 5.405 7.919 8.314 1.00 0.00 WT1 H -ATOM 96 H2 TIP3W 485 4.002 8.458 8.422 1.00 0.00 WT1 H -ATOM 97 OH2 TIP3W 486 3.403 4.687 9.815 1.00 0.00 WT1 O -ATOM 98 H1 TIP3W 486 3.109 5.272 9.097 1.00 0.00 WT1 H -ATOM 99 H2 TIP3W 486 3.817 3.973 9.327 1.00 0.00 WT1 H -ATOM 100 OH2 TIP3W 489 3.276 7.465 19.325 1.00 0.00 WT1 O -ATOM 101 H1 TIP3W 489 2.772 6.991 19.964 1.00 0.00 WT1 H -ATOM 102 H2 TIP3W 489 3.604 8.288 19.753 1.00 0.00 WT1 H -ATOM 103 OH2 TIP3W 503 3.119 10.325 13.158 1.00 0.00 WT1 O -ATOM 104 H1 TIP3W 503 3.598 10.900 12.512 1.00 0.00 WT1 H -ATOM 105 H2 TIP3W 503 3.440 9.430 12.962 1.00 0.00 WT1 H -ATOM 106 OH2 TIP3W 506 2.378 5.806 16.253 1.00 0.00 WT1 O -ATOM 107 H1 TIP3W 506 2.157 6.161 17.099 1.00 0.00 WT1 H -ATOM 108 H2 TIP3W 506 3.301 6.032 16.126 1.00 0.00 WT1 H -ATOM 109 OH2 TIP3W 507 6.382 22.271 2.319 1.00 0.00 WT1 O -ATOM 110 H1 TIP3W 507 5.550 22.035 1.847 1.00 0.00 WT1 H -ATOM 111 H2 TIP3W 507 6.859 21.472 2.192 1.00 0.00 WT1 H -ATOM 112 OH2 TIP3W 509 4.017 3.905 19.418 1.00 0.00 WT1 O -ATOM 113 H1 TIP3W 509 3.142 4.042 19.132 1.00 0.00 WT1 H -ATOM 114 H2 TIP3W 509 4.582 4.727 19.295 1.00 0.00 WT1 H -ATOM 115 OH2 TIP3W 511 2.344 20.472 21.631 1.00 0.00 WT1 O -ATOM 116 H1 TIP3W 511 2.932 20.821 20.945 1.00 0.00 WT1 H -ATOM 117 H2 TIP3W 511 1.467 20.548 21.138 1.00 0.00 WT1 H -ATOM 118 OH2 TIP3W 517 14.526 10.532 20.137 1.00 0.00 WT1 O -ATOM 119 H1 TIP3W 517 14.162 9.733 20.503 1.00 0.00 WT1 H -ATOM 120 H2 TIP3W 517 14.466 10.420 19.194 1.00 0.00 WT1 H -ATOM 121 OH2 TIP3W 533 5.573 14.804 19.090 1.00 0.00 WT1 O -ATOM 122 H1 TIP3W 533 5.959 15.339 19.808 1.00 0.00 WT1 H -ATOM 123 H2 TIP3W 533 5.869 15.413 18.331 1.00 0.00 WT1 H -ATOM 124 OH2 TIP3W 543 5.458 13.097 4.589 1.00 0.00 WT1 O -ATOM 125 H1 TIP3W 543 5.673 13.019 3.612 1.00 0.00 WT1 H -ATOM 126 H2 TIP3W 543 4.899 13.894 4.657 1.00 0.00 WT1 H -ATOM 127 OH2 TIP3W 550 4.552 1.370 20.330 1.00 0.00 WT1 O -ATOM 128 H1 TIP3W 550 4.274 2.194 19.953 1.00 0.00 WT1 H -ATOM 129 H2 TIP3W 550 4.235 0.801 19.571 1.00 0.00 WT1 H -ATOM 130 OH2 TIP3W 554 5.160 13.744 7.954 1.00 0.00 WT1 O -ATOM 131 H1 TIP3W 554 6.048 13.422 8.207 1.00 0.00 WT1 H -ATOM 132 H2 TIP3W 554 5.008 14.493 8.528 1.00 0.00 WT1 H -ATOM 133 OH2 TIP3W 558 10.390 6.386 18.828 1.00 0.00 WT1 O -ATOM 134 H1 TIP3W 558 10.688 6.484 19.731 1.00 0.00 WT1 H -ATOM 135 H2 TIP3W 558 9.844 5.589 18.921 1.00 0.00 WT1 H -ATOM 136 OH2 TIP3W 562 1.678 21.942 1.035 1.00 0.00 WT1 O -ATOM 137 H1 TIP3W 562 1.272 21.280 1.592 1.00 0.00 WT1 H -ATOM 138 H2 TIP3W 562 1.498 22.809 1.493 1.00 0.00 WT1 H -ATOM 139 OH2 TIP3W 568 9.630 21.547 3.000 1.00 0.00 WT1 O -ATOM 140 H1 TIP3W 568 9.601 22.471 2.643 1.00 0.00 WT1 H -ATOM 141 H2 TIP3W 568 9.287 20.954 2.312 1.00 0.00 WT1 H -ATOM 142 OH2 TIP3W 575 2.344 10.571 2.624 1.00 0.00 WT1 O -ATOM 143 H1 TIP3W 575 2.122 10.753 3.553 1.00 0.00 WT1 H -ATOM 144 H2 TIP3W 575 2.947 9.791 2.617 1.00 0.00 WT1 H -ATOM 145 OH2 TIP3W 584 0.823 23.668 2.888 1.00 0.00 WT1 O -ATOM 146 H1 TIP3W 584 1.636 23.316 3.340 1.00 0.00 WT1 H -ATOM 147 H2 TIP3W 584 0.253 23.978 3.640 1.00 0.00 WT1 H -ATOM 148 OH2 TIP3W 594 2.710 6.185 7.540 1.00 0.00 WT1 O -ATOM 149 H1 TIP3W 594 2.467 6.236 6.561 1.00 0.00 WT1 H -ATOM 150 H2 TIP3W 594 3.410 6.855 7.580 1.00 0.00 WT1 H -ATOM 151 OH2 TIP3W 595 6.911 19.458 17.335 1.00 0.00 WT1 O -ATOM 152 H1 TIP3W 595 7.517 20.118 16.957 1.00 0.00 WT1 H -ATOM 153 H2 TIP3W 595 6.315 19.136 16.588 1.00 0.00 WT1 H -ATOM 154 OH2 TIP3W 613 13.540 22.220 2.748 1.00 0.00 WT1 O -ATOM 155 H1 TIP3W 613 12.965 22.475 3.462 1.00 0.00 WT1 H -ATOM 156 H2 TIP3W 613 14.428 22.404 3.074 1.00 0.00 WT1 H -ATOM 157 OH2 TIP3W 634 10.929 14.750 5.718 1.00 0.00 WT1 O -ATOM 158 H1 TIP3W 634 10.050 14.541 5.408 1.00 0.00 WT1 H -ATOM 159 H2 TIP3W 634 11.401 13.879 5.717 1.00 0.00 WT1 H -ATOM 160 OH2 TIP3W 822 0.747 4.469 10.579 1.00 0.00 WT1 O -ATOM 161 H1 TIP3W 822 0.426 3.568 10.339 1.00 0.00 WT1 H -ATOM 162 H2 TIP3W 822 1.505 4.585 9.990 1.00 0.00 WT1 H -ATOM 163 OH2 TIP3W 849 5.356 5.388 16.046 1.00 0.00 WT1 O -ATOM 164 H1 TIP3W 849 5.884 6.064 16.461 1.00 0.00 WT1 H -ATOM 165 H2 TIP3W 849 5.592 4.622 16.537 1.00 0.00 WT1 H -ATOM 166 OH2 TIP3W 867 10.704 6.721 15.883 1.00 0.00 WT1 O -ATOM 167 H1 TIP3W 867 10.901 6.912 16.836 1.00 0.00 WT1 H -ATOM 168 H2 TIP3W 867 10.127 5.972 15.998 1.00 0.00 WT1 H -ATOM 169 OH2 TIP3W 891 11.763 19.614 9.958 1.00 0.00 WT1 O -ATOM 170 H1 TIP3W 891 12.279 20.405 9.866 1.00 0.00 WT1 H -ATOM 171 H2 TIP3W 891 12.435 18.905 9.901 1.00 0.00 WT1 H -ATOM 172 OH2 TIP3W 906 7.027 2.224 13.411 1.00 0.00 WT1 O -ATOM 173 H1 TIP3W 906 6.185 2.801 13.535 1.00 0.00 WT1 H -ATOM 174 H2 TIP3W 906 6.692 1.403 13.742 1.00 0.00 WT1 H -ATOM 175 OH2 TIP3W 908 4.028 7.699 12.776 1.00 0.00 WT1 O -ATOM 176 H1 TIP3W 908 4.577 7.193 12.138 1.00 0.00 WT1 H -ATOM 177 H2 TIP3W 908 3.171 7.320 12.544 1.00 0.00 WT1 H -ATOM 178 OH2 TIP3W 924 12.493 9.451 2.215 1.00 0.00 WT1 O -ATOM 179 H1 TIP3W 924 12.908 9.840 2.987 1.00 0.00 WT1 H -ATOM 180 H2 TIP3W 924 12.982 8.641 2.039 1.00 0.00 WT1 H -ATOM 181 OH2 TIP3W 927 11.177 9.610 7.928 1.00 0.00 WT1 O -ATOM 182 H1 TIP3W 927 10.443 10.172 8.053 1.00 0.00 WT1 H -ATOM 183 H2 TIP3W 927 10.866 8.788 8.298 1.00 0.00 WT1 H -ATOM 184 OH2 TIP3W 928 1.838 3.206 15.398 1.00 0.00 WT1 O -ATOM 185 H1 TIP3W 928 2.201 4.081 15.545 1.00 0.00 WT1 H -ATOM 186 H2 TIP3W 928 2.117 2.999 14.422 1.00 0.00 WT1 H -ATOM 187 OH2 TIP3W 930 1.899 11.624 17.893 1.00 0.00 WT1 O -ATOM 188 H1 TIP3W 930 1.139 11.678 17.305 1.00 0.00 WT1 H -ATOM 189 H2 TIP3W 930 2.258 12.535 17.855 1.00 0.00 WT1 H -ATOM 190 OH2 TIP3W 932 9.220 13.904 17.340 1.00 0.00 WT1 O -ATOM 191 H1 TIP3W 932 10.062 14.198 17.738 1.00 0.00 WT1 H -ATOM 192 H2 TIP3W 932 9.394 12.999 17.102 1.00 0.00 WT1 H -ATOM 193 OH2 TIP3W 933 3.458 9.868 22.419 1.00 0.00 WT1 O -ATOM 194 H1 TIP3W 933 4.398 10.016 22.654 1.00 0.00 WT1 H -ATOM 195 H2 TIP3W 933 3.448 10.189 21.495 1.00 0.00 WT1 H -ATOM 196 OH2 TIP3W 947 15.430 3.274 7.407 1.00 0.00 WT1 O -ATOM 197 H1 TIP3W 947 15.458 2.741 8.157 1.00 0.00 WT1 H -ATOM 198 H2 TIP3W 947 15.933 2.740 6.770 1.00 0.00 WT1 H -ATOM 199 OH2 TIP3W 948 13.134 4.535 6.559 1.00 0.00 WT1 O -ATOM 200 H1 TIP3W 948 12.434 3.932 6.938 1.00 0.00 WT1 H -ATOM 201 H2 TIP3W 948 13.959 4.162 6.965 1.00 0.00 WT1 H -ATOM 202 OH2 TIP3W 951 10.295 14.066 14.320 1.00 0.00 WT1 O -ATOM 203 H1 TIP3W 951 10.592 14.067 15.226 1.00 0.00 WT1 H -ATOM 204 H2 TIP3W 951 9.322 14.226 14.350 1.00 0.00 WT1 H -ATOM 205 OH2 TIP3W 964 7.830 19.751 1.995 1.00 0.00 WT1 O -ATOM 206 H1 TIP3W 964 7.257 19.870 1.247 1.00 0.00 WT1 H -ATOM 207 H2 TIP3W 964 8.329 18.923 1.885 1.00 0.00 WT1 H -ATOM 208 OH2 TIP3W 972 15.027 11.249 9.806 1.00 0.00 WT1 O -ATOM 209 H1 TIP3W 972 15.636 10.953 9.104 1.00 0.00 WT1 H -ATOM 210 H2 TIP3W 972 14.929 12.194 9.545 1.00 0.00 WT1 H -ATOM 211 OH2 TIP3W 974 10.274 11.448 20.959 1.00 0.00 WT1 O -ATOM 212 H1 TIP3W 974 10.893 11.073 21.654 1.00 0.00 WT1 H -ATOM 213 H2 TIP3W 974 10.344 10.891 20.238 1.00 0.00 WT1 H -ATOM 214 OH2 TIP3W 975 11.473 6.075 21.702 1.00 0.00 WT1 O -ATOM 215 H1 TIP3W 975 12.046 5.667 22.431 1.00 0.00 WT1 H -ATOM 216 H2 TIP3W 975 10.554 5.939 22.100 1.00 0.00 WT1 H -ATOM 217 OH2 TIP3W 995 6.800 16.659 17.184 1.00 0.00 WT1 O -ATOM 218 H1 TIP3W 995 7.143 16.649 16.327 1.00 0.00 WT1 H -ATOM 219 H2 TIP3W 995 7.109 17.502 17.568 1.00 0.00 WT1 H -ATOM 220 OH2 TIP3W1007 14.603 18.110 3.213 1.00 0.00 WT1 O -ATOM 221 H1 TIP3W1007 14.275 17.655 3.963 1.00 0.00 WT1 H -ATOM 222 H2 TIP3W1007 13.842 18.606 2.878 1.00 0.00 WT1 H -ATOM 223 OH2 TIP3W1011 4.753 20.139 5.475 1.00 0.00 WT1 O -ATOM 224 H1 TIP3W1011 4.769 21.053 5.846 1.00 0.00 WT1 H -ATOM 225 H2 TIP3W1011 5.663 20.031 5.201 1.00 0.00 WT1 H -ATOM 226 OH2 TIP3W1013 1.615 17.355 14.355 1.00 0.00 WT1 O -ATOM 227 H1 TIP3W1013 1.225 16.480 14.420 1.00 0.00 WT1 H -ATOM 228 H2 TIP3W1013 0.859 17.984 14.051 1.00 0.00 WT1 H -ATOM 229 OH2 TIP3W1014 11.087 15.787 20.150 1.00 0.00 WT1 O -ATOM 230 H1 TIP3W1014 11.221 14.877 19.698 1.00 0.00 WT1 H -ATOM 231 H2 TIP3W1014 11.936 15.940 20.591 1.00 0.00 WT1 H -ATOM 232 OH2 TIP3W1017 9.784 18.060 16.439 1.00 0.00 WT1 O -ATOM 233 H1 TIP3W1017 10.576 18.166 15.922 1.00 0.00 WT1 H -ATOM 234 H2 TIP3W1017 9.941 18.584 17.234 1.00 0.00 WT1 H -ATOM 235 OH2 TIP3W1018 2.369 19.620 10.838 1.00 0.00 WT1 O -ATOM 236 H1 TIP3W1018 2.051 19.425 11.701 1.00 0.00 WT1 H -ATOM 237 H2 TIP3W1018 3.347 19.717 10.923 1.00 0.00 WT1 H -ATOM 238 OH2 TIP3W1027 15.158 15.218 1.453 1.00 0.00 WT1 O -ATOM 239 H1 TIP3W1027 15.286 16.123 1.160 1.00 0.00 WT1 H -ATOM 240 H2 TIP3W1027 14.175 15.219 1.587 1.00 0.00 WT1 H -ATOM 241 OH2 TIP3W1032 7.929 9.601 4.322 1.00 0.00 WT1 O -ATOM 242 H1 TIP3W1032 7.364 10.340 3.912 1.00 0.00 WT1 H -ATOM 243 H2 TIP3W1032 7.318 9.011 4.820 1.00 0.00 WT1 H -ATOM 244 OH2 TIP3W1053 11.585 23.121 19.455 1.00 0.00 WT1 O -ATOM 245 H1 TIP3W1053 12.413 23.205 19.982 1.00 0.00 WT1 H -ATOM 246 H2 TIP3W1053 10.816 23.266 20.095 1.00 0.00 WT1 H -ATOM 247 OH2 TIP3W1301 3.320 1.439 3.693 1.00 0.00 WT1 O -ATOM 248 H1 TIP3W1301 3.018 1.263 2.795 1.00 0.00 WT1 H -ATOM 249 H2 TIP3W1301 4.218 1.737 3.533 1.00 0.00 WT1 H -ATOM 250 OH2 TIP3W1308 8.378 22.836 14.074 1.00 0.00 WT1 O -ATOM 251 H1 TIP3W1308 9.127 23.085 13.478 1.00 0.00 WT1 H -ATOM 252 H2 TIP3W1308 7.806 23.652 14.112 1.00 0.00 WT1 H -ATOM 253 OH2 TIP3W1328 4.539 2.605 8.295 1.00 0.00 WT1 O -ATOM 254 H1 TIP3W1328 5.460 2.702 8.123 1.00 0.00 WT1 H -ATOM 255 H2 TIP3W1328 4.434 1.616 8.363 1.00 0.00 WT1 H -ATOM 256 OH2 TIP3W1344 8.883 21.581 5.760 1.00 0.00 WT1 O -ATOM 257 H1 TIP3W1344 8.705 22.232 6.446 1.00 0.00 WT1 H -ATOM 258 H2 TIP3W1344 9.357 22.008 5.077 1.00 0.00 WT1 H -ATOM 259 OH2 TIP3W1349 12.793 13.364 12.168 1.00 0.00 WT1 O -ATOM 260 H1 TIP3W1349 12.787 13.548 11.223 1.00 0.00 WT1 H -ATOM 261 H2 TIP3W1349 11.995 13.794 12.399 1.00 0.00 WT1 H -ATOM 262 OH2 TIP3W1352 6.667 7.547 9.646 1.00 0.00 WT1 O -ATOM 263 H1 TIP3W1352 6.103 6.975 10.296 1.00 0.00 WT1 H -ATOM 264 H2 TIP3W1352 7.558 7.292 10.046 1.00 0.00 WT1 H -ATOM 265 OH2 TIP3W1354 0.182 23.403 21.361 1.00 0.00 WT1 O -ATOM 266 H1 TIP3W1354 0.301 23.585 22.346 1.00 0.00 WT1 H -ATOM 267 H2 TIP3W1354 1.001 22.867 21.220 1.00 0.00 WT1 H -ATOM 268 OH2 TIP3W1355 11.347 16.007 23.148 1.00 0.00 WT1 O -ATOM 269 H1 TIP3W1355 11.779 15.126 23.087 1.00 0.00 WT1 H -ATOM 270 H2 TIP3W1355 10.586 15.923 22.581 1.00 0.00 WT1 H -ATOM 271 OH2 TIP3W1367 10.129 17.485 6.550 1.00 0.00 WT1 O -ATOM 272 H1 TIP3W1367 9.231 17.467 6.920 1.00 0.00 WT1 H -ATOM 273 H2 TIP3W1367 10.108 16.702 5.985 1.00 0.00 WT1 H -ATOM 274 OH2 TIP3W1370 4.654 5.717 5.023 1.00 0.00 WT1 O -ATOM 275 H1 TIP3W1370 5.059 5.126 4.395 1.00 0.00 WT1 H -ATOM 276 H2 TIP3W1370 5.409 5.785 5.634 1.00 0.00 WT1 H -ATOM 277 OH2 TIP3W1371 12.336 14.905 9.350 1.00 0.00 WT1 O -ATOM 278 H1 TIP3W1371 11.849 15.588 8.883 1.00 0.00 WT1 H -ATOM 279 H2 TIP3W1371 11.568 14.375 9.770 1.00 0.00 WT1 H -ATOM 280 OH2 TIP3W1374 5.488 14.255 13.212 1.00 0.00 WT1 O -ATOM 281 H1 TIP3W1374 6.279 14.126 13.709 1.00 0.00 WT1 H -ATOM 282 H2 TIP3W1374 4.864 13.991 13.878 1.00 0.00 WT1 H -ATOM 283 OH2 TIP3W1387 3.686 8.353 3.401 1.00 0.00 WT1 O -ATOM 284 H1 TIP3W1387 4.494 7.930 3.084 1.00 0.00 WT1 H -ATOM 285 H2 TIP3W1387 3.041 7.727 3.197 1.00 0.00 WT1 H -ATOM 286 OH2 TIP3W1388 15.005 14.526 19.133 1.00 0.00 WT1 O -ATOM 287 H1 TIP3W1388 15.742 13.941 19.238 1.00 0.00 WT1 H -ATOM 288 H2 TIP3W1388 14.746 14.453 18.188 1.00 0.00 WT1 H -ATOM 289 OH2 TIP3W1389 15.427 13.899 13.418 1.00 0.00 WT1 O -ATOM 290 H1 TIP3W1389 15.598 14.703 13.915 1.00 0.00 WT1 H -ATOM 291 H2 TIP3W1389 14.569 14.032 12.994 1.00 0.00 WT1 H -ATOM 292 OH2 TIP3W1392 15.117 16.342 15.320 1.00 0.00 WT1 O -ATOM 293 H1 TIP3W1392 14.190 16.658 15.235 1.00 0.00 WT1 H -ATOM 294 H2 TIP3W1392 15.725 17.080 14.950 1.00 0.00 WT1 H -ATOM 295 OH2 TIP3W1407 13.263 23.513 7.326 1.00 0.00 WT1 O -ATOM 296 H1 TIP3W1407 14.083 23.900 7.689 1.00 0.00 WT1 H -ATOM 297 H2 TIP3W1407 13.669 22.803 6.739 1.00 0.00 WT1 H -ATOM 298 OH2 TIP3W1411 10.030 11.441 3.434 1.00 0.00 WT1 O -ATOM 299 H1 TIP3W1411 9.274 10.827 3.422 1.00 0.00 WT1 H -ATOM 300 H2 TIP3W1411 10.533 11.362 2.661 1.00 0.00 WT1 H -ATOM 301 OH2 TIP3W1412 10.550 9.544 11.315 1.00 0.00 WT1 O -ATOM 302 H1 TIP3W1412 10.055 10.343 11.396 1.00 0.00 WT1 H -ATOM 303 H2 TIP3W1412 11.460 9.846 11.337 1.00 0.00 WT1 H -ATOM 304 OH2 TIP3W1414 2.005 17.796 21.122 1.00 0.00 WT1 O -ATOM 305 H1 TIP3W1414 2.773 17.325 21.598 1.00 0.00 WT1 H -ATOM 306 H2 TIP3W1414 2.173 18.758 21.265 1.00 0.00 WT1 H -ATOM 307 OH2 TIP3W1415 13.553 15.240 21.435 1.00 0.00 WT1 O -ATOM 308 H1 TIP3W1415 14.103 14.959 20.726 1.00 0.00 WT1 H -ATOM 309 H2 TIP3W1415 13.422 14.470 21.979 1.00 0.00 WT1 H -ATOM 310 OH2 TIP3W1418 11.456 2.350 19.585 1.00 0.00 WT1 O -ATOM 311 H1 TIP3W1418 10.731 2.931 19.730 1.00 0.00 WT1 H -ATOM 312 H2 TIP3W1418 11.546 1.862 20.401 1.00 0.00 WT1 H -ATOM 313 OH2 TIP3W1428 13.068 2.914 10.149 1.00 0.00 WT1 O -ATOM 314 H1 TIP3W1428 12.803 2.473 9.295 1.00 0.00 WT1 H -ATOM 315 H2 TIP3W1428 14.010 2.849 10.112 1.00 0.00 WT1 H -ATOM 316 OH2 TIP3W1429 5.450 9.067 5.337 1.00 0.00 WT1 O -ATOM 317 H1 TIP3W1429 4.722 8.840 4.711 1.00 0.00 WT1 H -ATOM 318 H2 TIP3W1429 4.939 8.770 6.117 1.00 0.00 WT1 H -ATOM 319 OH2 TIP3W1433 3.297 18.771 17.303 1.00 0.00 WT1 O -ATOM 320 H1 TIP3W1433 3.913 19.272 17.825 1.00 0.00 WT1 H -ATOM 321 H2 TIP3W1433 3.616 18.935 16.408 1.00 0.00 WT1 H -ATOM 322 OH2 TIP3W1435 6.597 15.954 21.463 1.00 0.00 WT1 O -ATOM 323 H1 TIP3W1435 7.157 15.160 21.200 1.00 0.00 WT1 H -ATOM 324 H2 TIP3W1435 7.205 16.451 22.021 1.00 0.00 WT1 H -ATOM 325 OH2 TIP3W1440 1.443 3.980 18.627 1.00 0.00 WT1 O -ATOM 326 H1 TIP3W1440 1.536 3.050 18.247 1.00 0.00 WT1 H -ATOM 327 H2 TIP3W1440 0.589 4.282 18.256 1.00 0.00 WT1 H -ATOM 328 OH2 TIP3W1451 3.248 22.876 3.701 1.00 0.00 WT1 O -ATOM 329 H1 TIP3W1451 2.662 22.334 4.248 1.00 0.00 WT1 H -ATOM 330 H2 TIP3W1451 4.106 22.410 3.781 1.00 0.00 WT1 H -ATOM 331 OH2 TIP3W1454 8.943 19.607 9.393 1.00 0.00 WT1 O -ATOM 332 H1 TIP3W1454 9.890 19.666 9.174 1.00 0.00 WT1 H -ATOM 333 H2 TIP3W1454 8.551 19.202 8.586 1.00 0.00 WT1 H -ATOM 334 OH2 TIP3W1455 7.534 23.313 22.010 1.00 0.00 WT1 O -ATOM 335 H1 TIP3W1455 7.309 22.777 22.738 1.00 0.00 WT1 H -ATOM 336 H2 TIP3W1455 6.697 23.403 21.532 1.00 0.00 WT1 H -ATOM 337 OH2 TIP3W1457 13.340 13.560 16.477 1.00 0.00 WT1 O -ATOM 338 H1 TIP3W1457 13.400 13.568 15.542 1.00 0.00 WT1 H -ATOM 339 H2 TIP3W1457 12.852 14.406 16.633 1.00 0.00 WT1 H -ATOM 340 OH2 TIP3W1458 8.344 7.845 20.429 1.00 0.00 WT1 O -ATOM 341 H1 TIP3W1458 8.479 8.292 21.236 1.00 0.00 WT1 H -ATOM 342 H2 TIP3W1458 9.102 8.059 19.900 1.00 0.00 WT1 H -ATOM 343 OH2 TIP3W1474 6.901 21.557 9.326 1.00 0.00 WT1 O -ATOM 344 H1 TIP3W1474 7.410 20.744 9.384 1.00 0.00 WT1 H -ATOM 345 H2 TIP3W1474 7.474 22.077 8.759 1.00 0.00 WT1 H -ATOM 346 OH2 TIP3W1494 14.403 7.815 15.212 1.00 0.00 WT1 O -ATOM 347 H1 TIP3W1494 13.532 8.206 14.911 1.00 0.00 WT1 H -ATOM 348 H2 TIP3W1494 14.885 7.681 14.373 1.00 0.00 WT1 H -ATOM 349 OH2 TIP3W1497 6.857 11.138 6.829 1.00 0.00 WT1 O -ATOM 350 H1 TIP3W1497 6.107 11.750 6.800 1.00 0.00 WT1 H -ATOM 351 H2 TIP3W1497 6.480 10.387 6.353 1.00 0.00 WT1 H -ATOM 352 OH2 TIP3W1512 10.309 21.500 11.481 1.00 0.00 WT1 O -ATOM 353 H1 TIP3W1512 11.014 20.928 11.185 1.00 0.00 WT1 H -ATOM 354 H2 TIP3W1512 9.595 20.961 11.183 1.00 0.00 WT1 H -ATOM 355 OH2 TIP3W1532 13.235 22.943 15.633 1.00 0.00 WT1 O -ATOM 356 H1 TIP3W1532 12.613 22.525 16.194 1.00 0.00 WT1 H -ATOM 357 H2 TIP3W1532 14.027 22.981 16.180 1.00 0.00 WT1 H -ATOM 358 OH2 TIP3W1559 6.818 20.066 20.150 1.00 0.00 WT1 O -ATOM 359 H1 TIP3W1559 7.686 20.067 20.626 1.00 0.00 WT1 H -ATOM 360 H2 TIP3W1559 6.969 19.869 19.212 1.00 0.00 WT1 H -ATOM 361 OH2 TIP3W1611 7.975 20.030 22.745 1.00 0.00 WT1 O -ATOM 362 H1 TIP3W1611 8.632 20.654 22.435 1.00 0.00 WT1 H -ATOM 363 H2 TIP3W1611 7.441 20.490 23.501 1.00 0.00 WT1 H -ATOM 364 OH2 TIP3W1707 12.113 0.921 4.942 1.00 0.00 WT1 O -ATOM 365 H1 TIP3W1707 12.819 0.635 5.562 1.00 0.00 WT1 H -ATOM 366 H2 TIP3W1707 11.814 1.896 5.223 1.00 0.00 WT1 H -ATOM 367 OH2 TIP3W1723 9.197 4.375 15.964 1.00 0.00 WT1 O -ATOM 368 H1 TIP3W1723 9.163 3.590 15.387 1.00 0.00 WT1 H -ATOM 369 H2 TIP3W1723 8.516 4.167 16.604 1.00 0.00 WT1 H -ATOM 370 OH2 TIP3W1725 2.421 3.775 5.058 1.00 0.00 WT1 O -ATOM 371 H1 TIP3W1725 2.684 2.934 4.652 1.00 0.00 WT1 H -ATOM 372 H2 TIP3W1725 3.219 4.340 5.048 1.00 0.00 WT1 H -ATOM 373 OH2 TIP3W1729 6.794 6.875 22.997 1.00 0.00 WT1 O -ATOM 374 H1 TIP3W1729 7.166 7.815 23.093 1.00 0.00 WT1 H -ATOM 375 H2 TIP3W1729 5.834 7.029 23.036 1.00 0.00 WT1 H -ATOM 376 OH2 TIP3W1730 11.518 2.141 14.835 1.00 0.00 WT1 O -ATOM 377 H1 TIP3W1730 11.356 2.769 14.101 1.00 0.00 WT1 H -ATOM 378 H2 TIP3W1730 12.345 1.727 14.583 1.00 0.00 WT1 H -ATOM 379 OH2 TIP3W1733 3.174 1.584 16.976 1.00 0.00 WT1 O -ATOM 380 H1 TIP3W1733 2.370 2.077 16.810 1.00 0.00 WT1 H -ATOM 381 H2 TIP3W1733 3.270 0.961 16.252 1.00 0.00 WT1 H -ATOM 382 OH2 TIP3W1746 10.848 10.071 18.631 1.00 0.00 WT1 O -ATOM 383 H1 TIP3W1746 10.345 10.477 17.907 1.00 0.00 WT1 H -ATOM 384 H2 TIP3W1746 11.663 10.551 18.638 1.00 0.00 WT1 H -ATOM 385 OH2 TIP3W1752 12.069 8.766 23.082 1.00 0.00 WT1 O -ATOM 386 H1 TIP3W1752 12.023 9.290 23.888 1.00 0.00 WT1 H -ATOM 387 H2 TIP3W1752 11.590 7.956 23.400 1.00 0.00 WT1 H -ATOM 388 OH2 TIP3W1764 5.141 1.611 0.499 1.00 0.00 WT1 O -ATOM 389 H1 TIP3W1764 4.697 1.110 1.234 1.00 0.00 WT1 H -ATOM 390 H2 TIP3W1764 6.031 1.302 0.586 1.00 0.00 WT1 H -ATOM 391 OH2 TIP3W1771 2.509 3.505 12.910 1.00 0.00 WT1 O -ATOM 392 H1 TIP3W1771 2.114 4.138 12.315 1.00 0.00 WT1 H -ATOM 393 H2 TIP3W1771 2.715 2.712 12.383 1.00 0.00 WT1 H -ATOM 394 OH2 TIP3W1773 14.354 1.352 14.004 1.00 0.00 WT1 O -ATOM 395 H1 TIP3W1773 14.694 0.623 14.565 1.00 0.00 WT1 H -ATOM 396 H2 TIP3W1773 14.573 2.195 14.426 1.00 0.00 WT1 H -ATOM 397 OH2 TIP3W1788 14.578 23.489 17.850 1.00 0.00 WT1 O -ATOM 398 H1 TIP3W1788 15.476 23.267 17.861 1.00 0.00 WT1 H -ATOM 399 H2 TIP3W1788 14.359 23.484 18.771 1.00 0.00 WT1 H -ATOM 400 OH2 TIP3W1789 5.461 6.754 1.943 1.00 0.00 WT1 O -ATOM 401 H1 TIP3W1789 6.412 6.627 2.018 1.00 0.00 WT1 H -ATOM 402 H2 TIP3W1789 5.209 5.956 1.434 1.00 0.00 WT1 H -ATOM 403 OH2 TIP3W1795 14.101 1.902 22.316 1.00 0.00 WT1 O -ATOM 404 H1 TIP3W1795 14.886 2.398 22.002 1.00 0.00 WT1 H -ATOM 405 H2 TIP3W1795 14.108 1.041 21.813 1.00 0.00 WT1 H -ATOM 406 OH2 TIP3W1813 6.142 11.858 16.052 1.00 0.00 WT1 O -ATOM 407 H1 TIP3W1813 5.762 12.642 15.675 1.00 0.00 WT1 H -ATOM 408 H2 TIP3W1813 5.566 11.146 15.661 1.00 0.00 WT1 H -ATOM 409 OH2 TIP3W1814 11.187 19.104 18.681 1.00 0.00 WT1 O -ATOM 410 H1 TIP3W1814 12.029 18.566 18.863 1.00 0.00 WT1 H -ATOM 411 H2 TIP3W1814 10.574 18.773 19.364 1.00 0.00 WT1 H -ATOM 412 OH2 TIP3W1829 11.780 13.509 0.983 1.00 0.00 WT1 O -ATOM 413 H1 TIP3W1829 12.311 13.422 1.794 1.00 0.00 WT1 H -ATOM 414 H2 TIP3W1829 12.379 13.816 0.300 1.00 0.00 WT1 H -ATOM 415 OH2 TIP3W1830 13.410 13.796 3.206 1.00 0.00 WT1 O -ATOM 416 H1 TIP3W1830 12.860 13.342 3.952 1.00 0.00 WT1 H -ATOM 417 H2 TIP3W1830 14.378 13.624 3.486 1.00 0.00 WT1 H -ATOM 418 OH2 TIP3W1831 7.314 0.228 9.152 1.00 0.00 WT1 O -ATOM 419 H1 TIP3W1831 7.447 0.196 8.157 1.00 0.00 WT1 H -ATOM 420 H2 TIP3W1831 8.219 0.336 9.426 1.00 0.00 WT1 H -ATOM 421 OH2 TIP3W1853 0.289 10.538 13.468 1.00 0.00 WT1 O -ATOM 422 H1 TIP3W1853 0.286 10.937 12.602 1.00 0.00 WT1 H -ATOM 423 H2 TIP3W1853 1.262 10.357 13.669 1.00 0.00 WT1 H -ATOM 424 OH2 TIP3W1856 12.440 12.407 5.370 1.00 0.00 WT1 O -ATOM 425 H1 TIP3W1856 11.652 11.887 5.105 1.00 0.00 WT1 H -ATOM 426 H2 TIP3W1856 12.893 11.867 5.977 1.00 0.00 WT1 H -ATOM 427 OH2 TIP3W1871 6.968 11.629 2.353 1.00 0.00 WT1 O -ATOM 428 H1 TIP3W1871 6.575 10.896 1.807 1.00 0.00 WT1 H -ATOM 429 H2 TIP3W1871 7.083 12.290 1.590 1.00 0.00 WT1 H -ATOM 430 OH2 TIP3W1873 13.533 10.550 7.160 1.00 0.00 WT1 O -ATOM 431 H1 TIP3W1873 12.608 10.309 7.490 1.00 0.00 WT1 H -ATOM 432 H2 TIP3W1873 14.008 10.940 7.925 1.00 0.00 WT1 H -ATOM 433 OH2 TIP3W1874 13.043 18.831 22.933 1.00 0.00 WT1 O -ATOM 434 H1 TIP3W1874 13.439 17.936 22.986 1.00 0.00 WT1 H -ATOM 435 H2 TIP3W1874 12.139 18.764 23.145 1.00 0.00 WT1 H -ATOM 436 OH2 TIP3W1894 11.706 15.811 16.829 1.00 0.00 WT1 O -ATOM 437 H1 TIP3W1894 10.892 16.347 16.590 1.00 0.00 WT1 H -ATOM 438 H2 TIP3W1894 12.344 16.466 17.162 1.00 0.00 WT1 H -ATOM 439 OH2 TIP3W1911 11.642 19.030 4.866 1.00 0.00 WT1 O -ATOM 440 H1 TIP3W1911 10.752 18.786 5.209 1.00 0.00 WT1 H -ATOM 441 H2 TIP3W1911 11.534 19.147 3.897 1.00 0.00 WT1 H -ATOM 442 OH2 TIP3W1912 13.550 21.522 9.565 1.00 0.00 WT1 O -ATOM 443 H1 TIP3W1912 13.279 21.744 8.655 1.00 0.00 WT1 H -ATOM 444 H2 TIP3W1912 13.859 22.419 9.914 1.00 0.00 WT1 H -ATOM 445 OH2 TIP3W1914 12.001 20.877 14.108 1.00 0.00 WT1 O -ATOM 446 H1 TIP3W1914 12.060 21.566 14.774 1.00 0.00 WT1 H -ATOM 447 H2 TIP3W1914 11.186 21.104 13.629 1.00 0.00 WT1 H -ATOM 448 OH2 TIP3W1915 12.814 17.906 7.383 1.00 0.00 WT1 O -ATOM 449 H1 TIP3W1915 13.379 17.410 6.688 1.00 0.00 WT1 H -ATOM 450 H2 TIP3W1915 11.963 17.994 6.954 1.00 0.00 WT1 H -ATOM 451 OH2 TIP3W1952 15.989 19.751 4.862 1.00 0.00 WT1 O -ATOM 452 H1 TIP3W1952 15.952 20.632 4.460 1.00 0.00 WT1 H -ATOM 453 H2 TIP3W1952 15.557 19.210 4.188 1.00 0.00 WT1 H -ATOM 454 OH2 TIP3W2123 10.963 1.737 11.790 1.00 0.00 WT1 O -ATOM 455 H1 TIP3W2123 10.319 2.240 11.334 1.00 0.00 WT1 H -ATOM 456 H2 TIP3W2123 11.709 2.167 11.210 1.00 0.00 WT1 H -ATOM 457 OH2 TIP3W2163 5.526 8.369 14.858 1.00 0.00 WT1 O -ATOM 458 H1 TIP3W2163 4.950 8.218 14.072 1.00 0.00 WT1 H -ATOM 459 H2 TIP3W2163 4.945 8.919 15.363 1.00 0.00 WT1 H -ATOM 460 OH2 TIP3W2165 14.776 4.939 12.443 1.00 0.00 WT1 O -ATOM 461 H1 TIP3W2165 14.636 5.952 12.252 1.00 0.00 WT1 H -ATOM 462 H2 TIP3W2165 13.865 4.712 12.604 1.00 0.00 WT1 H -ATOM 463 OH2 TIP3W2167 7.529 4.508 1.396 1.00 0.00 WT1 O -ATOM 464 H1 TIP3W2167 8.313 4.582 0.857 1.00 0.00 WT1 H -ATOM 465 H2 TIP3W2167 6.783 4.511 0.768 1.00 0.00 WT1 H -ATOM 466 OH2 TIP3W2172 11.435 0.836 22.059 1.00 0.00 WT1 O -ATOM 467 H1 TIP3W2172 11.858 0.103 21.657 1.00 0.00 WT1 H -ATOM 468 H2 TIP3W2172 12.219 1.281 22.508 1.00 0.00 WT1 H -ATOM 469 OH2 TIP3W2227 11.200 4.151 3.471 1.00 0.00 WT1 O -ATOM 470 H1 TIP3W2227 12.053 4.360 3.928 1.00 0.00 WT1 H -ATOM 471 H2 TIP3W2227 10.572 4.426 4.138 1.00 0.00 WT1 H -ATOM 472 OH2 TIP3W2231 4.884 4.081 13.713 1.00 0.00 WT1 O -ATOM 473 H1 TIP3W2231 4.970 4.746 14.373 1.00 0.00 WT1 H -ATOM 474 H2 TIP3W2231 3.932 3.975 13.593 1.00 0.00 WT1 H -ATOM 475 OH2 TIP3W2244 13.867 4.624 3.954 1.00 0.00 WT1 O -ATOM 476 H1 TIP3W2244 14.067 4.641 4.904 1.00 0.00 WT1 H -ATOM 477 H2 TIP3W2244 14.122 5.494 3.648 1.00 0.00 WT1 H -ATOM 478 OH2 TIP3W2270 3.174 11.159 5.954 1.00 0.00 WT1 O -ATOM 479 H1 TIP3W2270 3.904 11.073 5.352 1.00 0.00 WT1 H -ATOM 480 H2 TIP3W2270 3.204 12.104 6.129 1.00 0.00 WT1 H -ATOM 481 OH2 TIP3W2272 12.922 2.911 17.412 1.00 0.00 WT1 O -ATOM 482 H1 TIP3W2272 12.421 2.431 18.089 1.00 0.00 WT1 H -ATOM 483 H2 TIP3W2272 12.240 2.996 16.701 1.00 0.00 WT1 H -ATOM 484 OH2 TIP3W2277 13.644 7.961 20.946 1.00 0.00 WT1 O -ATOM 485 H1 TIP3W2277 13.183 7.158 20.680 1.00 0.00 WT1 H -ATOM 486 H2 TIP3W2277 13.018 8.315 21.687 1.00 0.00 WT1 H -ATOM 487 OH2 TIP3W2280 6.612 3.396 17.042 1.00 0.00 WT1 O -ATOM 488 H1 TIP3W2280 6.138 2.987 17.830 1.00 0.00 WT1 H -ATOM 489 H2 TIP3W2280 6.248 2.883 16.306 1.00 0.00 WT1 H -ATOM 490 OH2 TIP3W2288 3.628 15.453 9.684 1.00 0.00 WT1 O -ATOM 491 H1 TIP3W2288 3.604 16.368 9.365 1.00 0.00 WT1 H -ATOM 492 H2 TIP3W2288 3.266 15.478 10.592 1.00 0.00 WT1 H -ATOM 493 OH2 TIP3W2293 1.641 18.264 8.136 1.00 0.00 WT1 O -ATOM 494 H1 TIP3W2293 0.755 18.490 8.008 1.00 0.00 WT1 H -ATOM 495 H2 TIP3W2293 1.981 19.003 8.665 1.00 0.00 WT1 H -ATOM 496 OH2 TIP3W2295 8.716 0.819 21.571 1.00 0.00 WT1 O -ATOM 497 H1 TIP3W2295 8.359 0.399 22.460 1.00 0.00 WT1 H -ATOM 498 H2 TIP3W2295 9.622 1.046 21.690 1.00 0.00 WT1 H -ATOM 499 OH2 TIP3W2309 14.269 10.001 4.369 1.00 0.00 WT1 O -ATOM 500 H1 TIP3W2309 14.973 10.528 4.752 1.00 0.00 WT1 H -ATOM 501 H2 TIP3W2309 13.690 9.859 5.092 1.00 0.00 WT1 H -ATOM 502 OH2 TIP3W2311 14.691 13.817 9.050 1.00 0.00 WT1 O -ATOM 503 H1 TIP3W2311 15.162 14.372 8.385 1.00 0.00 WT1 H -ATOM 504 H2 TIP3W2311 13.821 14.250 9.113 1.00 0.00 WT1 H -ATOM 505 OH2 TIP3W2316 12.273 5.424 10.404 1.00 0.00 WT1 O -ATOM 506 H1 TIP3W2316 12.384 4.472 10.210 1.00 0.00 WT1 H -ATOM 507 H2 TIP3W2316 13.153 5.714 10.501 1.00 0.00 WT1 H -ATOM 508 OH2 TIP3W2317 3.759 13.253 15.143 1.00 0.00 WT1 O -ATOM 509 H1 TIP3W2317 3.552 13.546 16.059 1.00 0.00 WT1 H -ATOM 510 H2 TIP3W2317 2.862 13.321 14.740 1.00 0.00 WT1 H -ATOM 511 OH2 TIP3W2335 7.319 14.432 15.015 1.00 0.00 WT1 O -ATOM 512 H1 TIP3W2335 7.633 15.319 14.742 1.00 0.00 WT1 H -ATOM 513 H2 TIP3W2335 7.702 14.303 15.933 1.00 0.00 WT1 H -ATOM 514 OH2 TIP3W2357 3.117 11.819 10.070 1.00 0.00 WT1 O -ATOM 515 H1 TIP3W2357 3.490 12.496 9.523 1.00 0.00 WT1 H -ATOM 516 H2 TIP3W2357 3.937 11.583 10.539 1.00 0.00 WT1 H -ATOM 517 OH2 TIP3W2358 0.549 16.393 10.366 1.00 0.00 WT1 O -ATOM 518 H1 TIP3W2358 1.292 16.322 11.016 1.00 0.00 WT1 H -ATOM 519 H2 TIP3W2358 0.665 17.283 9.972 1.00 0.00 WT1 H -ATOM 520 OH2 TIP3W2607 10.050 5.605 5.758 1.00 0.00 WT1 O -ATOM 521 H1 TIP3W2607 10.155 6.554 5.556 1.00 0.00 WT1 H -ATOM 522 H2 TIP3W2607 10.797 5.389 6.309 1.00 0.00 WT1 H -ATOM 523 OH2 TIP3W2608 7.881 3.518 5.700 1.00 0.00 WT1 O -ATOM 524 H1 TIP3W2608 8.550 4.225 5.812 1.00 0.00 WT1 H -ATOM 525 H2 TIP3W2608 7.070 3.834 6.169 1.00 0.00 WT1 H -ATOM 526 OH2 TIP3W2634 8.559 3.515 11.535 1.00 0.00 WT1 O -ATOM 527 H1 TIP3W2634 8.435 4.298 12.155 1.00 0.00 WT1 H -ATOM 528 H2 TIP3W2634 7.955 2.899 11.952 1.00 0.00 WT1 H -ATOM 529 OH2 TIP3W2669 13.039 10.511 11.777 1.00 0.00 WT1 O -ATOM 530 H1 TIP3W2669 13.825 10.589 11.282 1.00 0.00 WT1 H -ATOM 531 H2 TIP3W2669 12.883 11.473 11.916 1.00 0.00 WT1 H -ATOM 532 OH2 TIP3W2691 15.316 3.976 15.033 1.00 0.00 WT1 O -ATOM 533 H1 TIP3W2691 15.353 4.265 14.065 1.00 0.00 WT1 H -ATOM 534 H2 TIP3W2691 14.585 4.533 15.460 1.00 0.00 WT1 H -ATOM 535 OH2 TIP3W2694 8.400 5.552 13.557 1.00 0.00 WT1 O -ATOM 536 H1 TIP3W2694 9.070 5.240 14.185 1.00 0.00 WT1 H -ATOM 537 H2 TIP3W2694 7.739 5.945 14.163 1.00 0.00 WT1 H -ATOM 538 OH2 TIP3W2714 4.281 21.161 19.066 1.00 0.00 WT1 O -ATOM 539 H1 TIP3W2714 5.157 21.058 19.381 1.00 0.00 WT1 H -ATOM 540 H2 TIP3W2714 4.169 22.110 18.904 1.00 0.00 WT1 H -ATOM 541 OH2 TIP3W2732 13.870 7.474 12.187 1.00 0.00 WT1 O -ATOM 542 H1 TIP3W2732 13.209 8.073 12.633 1.00 0.00 WT1 H -ATOM 543 H2 TIP3W2732 14.457 8.029 11.659 1.00 0.00 WT1 H -ATOM 544 OH2 TIP3W2735 13.600 17.247 9.998 1.00 0.00 WT1 O -ATOM 545 H1 TIP3W2735 13.256 16.385 10.107 1.00 0.00 WT1 H -ATOM 546 H2 TIP3W2735 13.616 17.337 9.047 1.00 0.00 WT1 H -ATOM 547 OH2 TIP3W2758 10.099 18.083 21.099 1.00 0.00 WT1 O -ATOM 548 H1 TIP3W2758 10.453 17.258 20.699 1.00 0.00 WT1 H -ATOM 549 H2 TIP3W2758 9.398 17.746 21.690 1.00 0.00 WT1 H -ATOM 550 OH2 TIP3W2778 15.465 7.955 17.814 1.00 0.00 WT1 O -ATOM 551 H1 TIP3W2778 15.150 7.979 16.932 1.00 0.00 WT1 H -ATOM 552 H2 TIP3W2778 14.706 7.563 18.306 1.00 0.00 WT1 H -ATOM 553 OH2 TIP3W3010 9.016 4.086 8.814 1.00 0.00 WT1 O -ATOM 554 H1 TIP3W3010 9.377 5.001 8.813 1.00 0.00 WT1 H -ATOM 555 H2 TIP3W3010 8.726 3.741 9.661 1.00 0.00 WT1 H -ATOM 556 OH2 TIP3W3072 6.439 5.144 7.455 1.00 0.00 WT1 O -ATOM 557 H1 TIP3W3072 7.310 4.836 7.837 1.00 0.00 WT1 H -ATOM 558 H2 TIP3W3072 6.121 5.819 8.116 1.00 0.00 WT1 H -ATOM 559 OH2 TIP3W3096 13.331 4.563 23.416 1.00 0.00 WT1 O -ATOM 560 H1 TIP3W3096 14.315 4.772 23.360 1.00 0.00 WT1 H -ATOM 561 H2 TIP3W3096 13.215 3.678 23.134 1.00 0.00 WT1 H -ATOM 562 OH2 TIP3W3134 11.401 21.480 17.136 1.00 0.00 WT1 O -ATOM 563 H1 TIP3W3134 11.522 22.112 17.856 1.00 0.00 WT1 H -ATOM 564 H2 TIP3W3134 11.255 20.672 17.636 1.00 0.00 WT1 H -ATOM 565 OH2 TIP3W3173 12.076 4.645 13.566 1.00 0.00 WT1 O -ATOM 566 H1 TIP3W3173 12.000 5.522 13.148 1.00 0.00 WT1 H -ATOM 567 H2 TIP3W3173 11.827 4.835 14.443 1.00 0.00 WT1 H -ATOM 568 OH2 TIP3W3177 9.131 1.075 15.841 1.00 0.00 WT1 O -ATOM 569 H1 TIP3W3177 9.948 1.463 15.412 1.00 0.00 WT1 H -ATOM 570 H2 TIP3W3177 9.113 0.161 15.464 1.00 0.00 WT1 H -ATOM 571 OH2 TIP3W3196 7.694 8.338 16.687 1.00 0.00 WT1 O -ATOM 572 H1 TIP3W3196 7.323 8.081 17.508 1.00 0.00 WT1 H -ATOM 573 H2 TIP3W3196 6.991 8.476 16.072 1.00 0.00 WT1 H -ATOM 574 OH2 TIP3W3218 11.912 13.212 19.726 1.00 0.00 WT1 O -ATOM 575 H1 TIP3W3218 12.854 13.225 19.881 1.00 0.00 WT1 H -ATOM 576 H2 TIP3W3218 11.504 12.764 20.555 1.00 0.00 WT1 H -ATOM 577 OH2 TIP3W3223 5.115 19.820 22.632 1.00 0.00 WT1 O -ATOM 578 H1 TIP3W3223 4.270 19.752 22.092 1.00 0.00 WT1 H -ATOM 579 H2 TIP3W3223 5.800 19.585 21.996 1.00 0.00 WT1 H -ATOM 580 OH2 TIP3W3303 14.170 23.047 20.478 1.00 0.00 WT1 O -ATOM 581 H1 TIP3W3303 15.015 22.883 20.902 1.00 0.00 WT1 H -ATOM 582 H2 TIP3W3303 13.757 22.177 20.579 1.00 0.00 WT1 H -ATOM 583 OH2 TIP3W3304 13.163 20.489 20.636 1.00 0.00 WT1 O -ATOM 584 H1 TIP3W3304 12.450 20.171 20.104 1.00 0.00 WT1 H -ATOM 585 H2 TIP3W3304 13.220 19.875 21.393 1.00 0.00 WT1 H -ATOM 586 OH2 TIP3W3447 11.316 2.273 7.956 1.00 0.00 WT1 O -ATOM 587 H1 TIP3W3447 11.391 1.358 8.151 1.00 0.00 WT1 H -ATOM 588 H2 TIP3W3447 10.423 2.479 8.181 1.00 0.00 WT1 H -ATOM 589 OH2 TIP3W3545 10.407 6.649 8.888 1.00 0.00 WT1 O -ATOM 590 H1 TIP3W3545 9.810 7.215 9.386 1.00 0.00 WT1 H -ATOM 591 H2 TIP3W3545 11.077 6.417 9.547 1.00 0.00 WT1 H -ATOM 592 OH2 TIP3W3596 7.574 19.420 4.717 1.00 0.00 WT1 O -ATOM 593 H1 TIP3W3596 7.704 19.335 3.679 1.00 0.00 WT1 H -ATOM 594 H2 TIP3W3596 7.970 20.255 4.957 1.00 0.00 WT1 H -ATOM 595 OH2 TIP3W3650 12.254 19.676 2.229 1.00 0.00 WT1 O -ATOM 596 H1 TIP3W3650 12.678 20.538 2.358 1.00 0.00 WT1 H -ATOM 597 H2 TIP3W3650 12.115 19.535 1.250 1.00 0.00 WT1 H -ATOM 598 OH2 TIP3W3660 14.036 7.730 6.644 1.00 0.00 WT1 O -ATOM 599 H1 TIP3W3660 14.358 7.138 7.346 1.00 0.00 WT1 H -ATOM 600 H2 TIP3W3660 13.886 8.589 7.123 1.00 0.00 WT1 H -ATOM 601 OH2 TIP3W3977 8.900 7.310 11.290 1.00 0.00 WT1 O -ATOM 602 H1 TIP3W3977 8.739 6.706 12.078 1.00 0.00 WT1 H -ATOM 603 H2 TIP3W3977 9.555 8.003 11.531 1.00 0.00 WT1 H -ATOM 604 OH2 TIP3W4012 9.495 14.416 1.979 1.00 0.00 WT1 O -ATOM 605 H1 TIP3W4012 10.354 14.203 1.548 1.00 0.00 WT1 H -ATOM 606 H2 TIP3W4012 9.165 13.566 2.099 1.00 0.00 WT1 H -ATOM 607 OH2 TIP3W4036 13.605 5.353 19.280 1.00 0.00 WT1 O -ATOM 608 H1 TIP3W4036 13.658 4.527 18.812 1.00 0.00 WT1 H -ATOM 609 H2 TIP3W4036 12.688 5.367 19.516 1.00 0.00 WT1 H -ATOM 610 OH2 TIP3W4074 7.334 17.973 7.090 1.00 0.00 WT1 O -ATOM 611 H1 TIP3W4074 7.571 18.390 6.200 1.00 0.00 WT1 H -ATOM 612 H2 TIP3W4074 6.533 17.444 6.885 1.00 0.00 WT1 H -ATOM 613 OH2 TIP3W4077 13.912 11.040 17.383 1.00 0.00 WT1 O -ATOM 614 H1 TIP3W4077 13.913 10.932 16.423 1.00 0.00 WT1 H -ATOM 615 H2 TIP3W4077 13.612 11.935 17.518 1.00 0.00 WT1 H -ATOM 616 OH2 TIP3W4501 14.682 11.334 14.388 1.00 0.00 WT1 O -ATOM 617 H1 TIP3W4501 15.236 11.941 13.876 1.00 0.00 WT1 H -ATOM 618 H2 TIP3W4501 14.266 10.683 13.763 1.00 0.00 WT1 H -ATOM 619 OH2 TIP3W4515 12.414 9.004 13.909 1.00 0.00 WT1 O -ATOM 620 H1 TIP3W4515 11.523 8.931 14.184 1.00 0.00 WT1 H -ATOM 621 H2 TIP3W4515 12.375 9.766 13.286 1.00 0.00 WT1 H -ATOM 622 OH2 TIP3W4809 15.898 3.293 1.648 1.00 0.00 WT1 O -ATOM 623 H1 TIP3W4809 15.837 3.977 2.359 1.00 0.00 WT1 H -ATOM 624 H2 TIP3W4809 15.065 2.796 1.789 1.00 0.00 WT1 H -ATOM 625 OH2 TIP3W6240 3.080 0.949 11.788 1.00 0.00 WT1 O -ATOM 626 H1 TIP3W6240 3.690 0.500 11.172 1.00 0.00 WT1 H -ATOM 627 H2 TIP3W6240 2.196 0.556 11.641 1.00 0.00 WT1 H -ATOM 628 OH2 TIP3W6671 0.897 12.813 20.940 1.00 0.00 WT1 O -ATOM 629 H1 TIP3W6671 1.234 13.577 21.489 1.00 0.00 WT1 H -ATOM 630 H2 TIP3W6671 1.110 12.083 21.442 1.00 0.00 WT1 H -ATOM 631 OH2 TIP3W7222 6.255 9.802 0.364 1.00 0.00 WT1 O -ATOM 632 H1 TIP3W7222 6.954 9.121 0.671 1.00 0.00 WT1 H -ATOM 633 H2 TIP3W7222 5.459 9.264 0.196 1.00 0.00 WT1 H -ATOM 634 OH2 TIP3W7479 6.140 3.669 3.704 1.00 0.00 WT1 O -ATOM 635 H1 TIP3W7479 6.732 3.837 2.949 1.00 0.00 WT1 H -ATOM 636 H2 TIP3W7479 6.807 3.408 4.378 1.00 0.00 WT1 H -ATOM 637 OH2 TIP3W7510 5.150 11.685 11.994 1.00 0.00 WT1 O -ATOM 638 H1 TIP3W7510 5.312 12.641 12.020 1.00 0.00 WT1 H -ATOM 639 H2 TIP3W7510 5.614 11.405 12.778 1.00 0.00 WT1 H -ATOM 640 OH2 TIP3W7563 5.196 19.304 15.315 1.00 0.00 WT1 O -ATOM 641 H1 TIP3W7563 5.227 20.213 14.942 1.00 0.00 WT1 H -ATOM 642 H2 TIP3W7563 5.252 18.720 14.569 1.00 0.00 WT1 H -ATOM 643 OH2 TIP3W7630 2.179 13.464 7.177 1.00 0.00 WT1 O -ATOM 644 H1 TIP3W7630 2.719 14.061 7.737 1.00 0.00 WT1 H -ATOM 645 H2 TIP3W7630 1.640 13.021 7.843 1.00 0.00 WT1 H -ATOM 646 OH2 TIP3W7631 1.926 21.439 17.027 1.00 0.00 WT1 O -ATOM 647 H1 TIP3W7631 2.672 21.817 16.545 1.00 0.00 WT1 H -ATOM 648 H2 TIP3W7631 2.398 20.912 17.662 1.00 0.00 WT1 H -ATOM 649 OH2 TIP3W7707 0.688 2.781 7.114 1.00 0.00 WT1 O -ATOM 650 H1 TIP3W7707 1.488 3.190 6.703 1.00 0.00 WT1 H -ATOM 651 H2 TIP3W7707 0.053 3.429 6.930 1.00 0.00 WT1 H -ATOM 652 OH2 TIP3W7985 0.449 7.366 9.140 1.00 0.00 WT1 O -ATOM 653 H1 TIP3W7985 0.202 6.479 9.095 1.00 0.00 WT1 H -ATOM 654 H2 TIP3W7985 0.796 7.563 8.256 1.00 0.00 WT1 H -ATOM 655 OH2 TIP3W8023 0.913 12.320 0.937 1.00 0.00 WT1 O -ATOM 656 H1 TIP3W8023 0.623 11.700 0.268 1.00 0.00 WT1 H -ATOM 657 H2 TIP3W8023 1.290 11.784 1.628 1.00 0.00 WT1 H -ATOM 658 OH2 TIP3W8029 7.889 16.997 14.360 1.00 0.00 WT1 O -ATOM 659 H1 TIP3W8029 7.935 17.181 13.358 1.00 0.00 WT1 H -ATOM 660 H2 TIP3W8029 8.602 17.562 14.734 1.00 0.00 WT1 H -ATOM 661 OH2 TIP3W8046 3.230 22.882 11.736 1.00 0.00 WT1 O -ATOM 662 H1 TIP3W8046 3.601 21.950 11.670 1.00 0.00 WT1 H -ATOM 663 H2 TIP3W8046 2.861 22.992 10.853 1.00 0.00 WT1 H -ATOM 664 OH2 TIP3W8064 4.620 22.335 7.130 1.00 0.00 WT1 O -ATOM 665 H1 TIP3W8064 3.754 22.591 7.590 1.00 0.00 WT1 H -ATOM 666 H2 TIP3W8064 5.178 22.349 7.907 1.00 0.00 WT1 H -ATOM 667 OH2 TIP3W8068 1.124 22.962 13.514 1.00 0.00 WT1 O -ATOM 668 H1 TIP3W8068 1.837 22.901 12.860 1.00 0.00 WT1 H -ATOM 669 H2 TIP3W8068 0.685 23.799 13.310 1.00 0.00 WT1 H -ATOM 670 OH2 TIP3W8364 8.561 10.924 16.881 1.00 0.00 WT1 O -ATOM 671 H1 TIP3W8364 7.916 11.188 16.202 1.00 0.00 WT1 H -ATOM 672 H2 TIP3W8364 8.309 10.008 17.123 1.00 0.00 WT1 H -ATOM 673 OH2 TIP3W8403 4.751 19.009 2.814 1.00 0.00 WT1 O -ATOM 674 H1 TIP3W8403 4.754 18.978 3.760 1.00 0.00 WT1 H -ATOM 675 H2 TIP3W8403 5.300 18.306 2.612 1.00 0.00 WT1 H -ATOM 676 OH2 TIP3W8411 3.406 0.117 14.493 1.00 0.00 WT1 O -ATOM 677 H1 TIP3W8411 3.348 0.244 13.546 1.00 0.00 WT1 H -ATOM 678 H2 TIP3W8411 4.378 0.190 14.724 1.00 0.00 WT1 H -ATOM 679 OH2 TIP3W8425 2.278 3.922 1.200 1.00 0.00 WT1 O -ATOM 680 H1 TIP3W8425 2.701 3.392 0.560 1.00 0.00 WT1 H -ATOM 681 H2 TIP3W8425 1.556 3.406 1.415 1.00 0.00 WT1 H -ATOM 682 OH2 TIP3W8441 6.246 21.216 13.564 1.00 0.00 WT1 O -ATOM 683 H1 TIP3W8441 7.127 21.533 13.794 1.00 0.00 WT1 H -ATOM 684 H2 TIP3W8441 5.802 22.075 13.455 1.00 0.00 WT1 H -ATOM 685 OH2 TIP3W8466 5.348 15.459 5.988 1.00 0.00 WT1 O -ATOM 686 H1 TIP3W8466 4.942 16.211 6.465 1.00 0.00 WT1 H -ATOM 687 H2 TIP3W8466 4.964 14.679 6.422 1.00 0.00 WT1 H -ATOM 688 OH2 TIP3W8468 1.312 13.577 13.829 1.00 0.00 WT1 O -ATOM 689 H1 TIP3W8468 1.594 13.350 12.963 1.00 0.00 WT1 H -ATOM 690 H2 TIP3W8468 0.905 14.443 13.634 1.00 0.00 WT1 H -ATOM 691 OH2 TIP3W8491 10.395 21.375 22.397 1.00 0.00 WT1 O -ATOM 692 H1 TIP3W8491 10.900 20.680 22.794 1.00 0.00 WT1 H -ATOM 693 H2 TIP3W8491 10.682 22.154 22.828 1.00 0.00 WT1 H -ATOM 694 OH2 TIP3W8528 6.013 16.085 3.326 1.00 0.00 WT1 O -ATOM 695 H1 TIP3W8528 6.016 16.035 4.292 1.00 0.00 WT1 H -ATOM 696 H2 TIP3W8528 5.249 15.516 3.046 1.00 0.00 WT1 H -ATOM 697 OH2 TIP3W8534 2.184 22.110 9.500 1.00 0.00 WT1 O -ATOM 698 H1 TIP3W8534 1.913 21.297 9.998 1.00 0.00 WT1 H -ATOM 699 H2 TIP3W8534 1.389 22.233 8.964 1.00 0.00 WT1 H -ATOM 700 OH2 TIP3W8536 3.207 13.979 17.772 1.00 0.00 WT1 O -ATOM 701 H1 TIP3W8536 3.947 14.082 18.373 1.00 0.00 WT1 H -ATOM 702 H2 TIP3W8536 2.585 14.685 17.921 1.00 0.00 WT1 H -ATOM 703 OH2 TIP3W8548 13.639 16.098 5.269 1.00 0.00 WT1 O -ATOM 704 H1 TIP3W8548 14.099 15.394 4.872 1.00 0.00 WT1 H -ATOM 705 H2 TIP3W8548 12.755 15.724 5.343 1.00 0.00 WT1 H -ATOM 706 OH2 TIP3W8556 1.981 16.635 18.663 1.00 0.00 WT1 O -ATOM 707 H1 TIP3W8556 1.921 17.181 19.529 1.00 0.00 WT1 H -ATOM 708 H2 TIP3W8556 2.656 17.117 18.156 1.00 0.00 WT1 H -ATOM 709 OH2 TIP3W8760 13.457 20.491 6.545 1.00 0.00 WT1 O -ATOM 710 H1 TIP3W8760 13.544 19.713 6.959 1.00 0.00 WT1 H -ATOM 711 H2 TIP3W8760 13.199 20.170 5.601 1.00 0.00 WT1 H -ATOM 712 OH2 TIP3W8780 3.438 8.099 0.316 1.00 0.00 WT1 O -ATOM 713 H1 TIP3W8780 2.547 7.847 0.577 1.00 0.00 WT1 H -ATOM 714 H2 TIP3W8780 3.889 7.775 1.093 1.00 0.00 WT1 H -ATOM 715 OH2 TIP3W8801 9.016 15.690 9.485 1.00 0.00 WT1 O -ATOM 716 H1 TIP3W8801 9.158 14.769 9.701 1.00 0.00 WT1 H -ATOM 717 H2 TIP3W8801 8.537 15.554 8.652 1.00 0.00 WT1 H -ATOM 718 OH2 TIP3W8822 1.562 6.536 12.239 1.00 0.00 WT1 O -ATOM 719 H1 TIP3W8822 0.960 7.250 12.049 1.00 0.00 WT1 H -ATOM 720 H2 TIP3W8822 1.197 5.827 11.553 1.00 0.00 WT1 H -ATOM 721 OH2 TIP3W8829 1.314 9.385 7.173 1.00 0.00 WT1 O -ATOM 722 H1 TIP3W8829 1.333 8.706 6.444 1.00 0.00 WT1 H -ATOM 723 H2 TIP3W8829 2.056 9.953 6.980 1.00 0.00 WT1 H -ATOM 724 OH2 TIP3W8843 7.572 0.420 3.478 1.00 0.00 WT1 O -ATOM 725 H1 TIP3W8843 7.636 0.339 2.503 1.00 0.00 WT1 H -ATOM 726 H2 TIP3W8843 6.628 0.234 3.530 1.00 0.00 WT1 H -ATOM 727 OH2 TIP3W8845 1.133 7.080 5.078 1.00 0.00 WT1 O -ATOM 728 H1 TIP3W8845 1.201 7.102 4.137 1.00 0.00 WT1 H -ATOM 729 H2 TIP3W8845 0.358 6.549 5.302 1.00 0.00 WT1 H -ATOM 730 OH2 TIP3W8865 11.515 22.342 4.827 1.00 0.00 WT1 O -ATOM 731 H1 TIP3W8865 10.875 21.911 4.185 1.00 0.00 WT1 H -ATOM 732 H2 TIP3W8865 11.205 21.919 5.694 1.00 0.00 WT1 H -ATOM 733 OH2 TIP3W8869 5.279 5.755 11.457 1.00 0.00 WT1 O -ATOM 734 H1 TIP3W8869 4.504 5.333 10.967 1.00 0.00 WT1 H -ATOM 735 H2 TIP3W8869 5.564 4.986 12.019 1.00 0.00 WT1 H -ATOM 736 OH2 TIP3W8887 8.890 21.041 16.070 1.00 0.00 WT1 O -ATOM 737 H1 TIP3W8887 8.698 21.572 15.300 1.00 0.00 WT1 H -ATOM 738 H2 TIP3W8887 9.800 21.340 16.244 1.00 0.00 WT1 H -ATOM 739 OH2 TIP3W8895 6.000 11.283 22.324 1.00 0.00 WT1 O -ATOM 740 H1 TIP3W8895 5.866 12.057 22.939 1.00 0.00 WT1 H -ATOM 741 H2 TIP3W8895 5.863 11.634 21.452 1.00 0.00 WT1 H -ATOM 742 OH2 TIP3W8905 7.834 14.408 7.527 1.00 0.00 WT1 O -ATOM 743 H1 TIP3W8905 7.105 14.717 6.993 1.00 0.00 WT1 H -ATOM 744 H2 TIP3W8905 8.194 13.714 6.926 1.00 0.00 WT1 H -ATOM 745 OH2 TIP3W8931 5.667 11.812 19.542 1.00 0.00 WT1 O -ATOM 746 H1 TIP3W8931 5.647 12.743 19.497 1.00 0.00 WT1 H -ATOM 747 H2 TIP3W8931 5.889 11.629 18.618 1.00 0.00 WT1 H -ATOM 748 OH2 TIP3W8932 12.997 18.576 15.207 1.00 0.00 WT1 O -ATOM 749 H1 TIP3W8932 12.617 19.193 14.493 1.00 0.00 WT1 H -ATOM 750 H2 TIP3W8932 13.582 19.163 15.737 1.00 0.00 WT1 H -ATOM 751 OH2 TIP3W8935 0.675 11.574 10.952 1.00 0.00 WT1 O -ATOM 752 H1 TIP3W8935 1.597 11.546 10.574 1.00 0.00 WT1 H -ATOM 753 H2 TIP3W8935 0.265 12.150 10.339 1.00 0.00 WT1 H -ATOM 754 OH2 TIP3W8949 8.782 17.187 2.362 1.00 0.00 WT1 O -ATOM 755 H1 TIP3W8949 8.004 16.786 2.797 1.00 0.00 WT1 H -ATOM 756 H2 TIP3W8949 9.140 16.422 1.970 1.00 0.00 WT1 H -ATOM 757 OH2 TIP3W8956 2.113 6.516 21.893 1.00 0.00 WT1 O -ATOM 758 H1 TIP3W8956 2.170 5.576 22.160 1.00 0.00 WT1 H -ATOM 759 H2 TIP3W8956 2.446 6.949 22.707 1.00 0.00 WT1 H -ATOM 760 OH2 TIP3W8977 2.583 16.123 12.046 1.00 0.00 WT1 O -ATOM 761 H1 TIP3W8977 3.491 16.508 12.059 1.00 0.00 WT1 H -ATOM 762 H2 TIP3W8977 2.312 16.312 12.887 1.00 0.00 WT1 H -ATOM 763 OH2 TIP3W8988 2.246 20.883 4.995 1.00 0.00 WT1 O -ATOM 764 H1 TIP3W8988 1.611 20.097 4.885 1.00 0.00 WT1 H -ATOM 765 H2 TIP3W8988 3.079 20.473 5.195 1.00 0.00 WT1 H -ATOM 766 OH2 TIP3W9082 8.156 17.564 11.520 1.00 0.00 WT1 O -ATOM 767 H1 TIP3W9082 8.355 18.345 10.921 1.00 0.00 WT1 H -ATOM 768 H2 TIP3W9082 8.334 16.820 10.874 1.00 0.00 WT1 H -ATOM 769 OH2 TIP3W9096 2.915 14.197 3.393 1.00 0.00 WT1 O -ATOM 770 H1 TIP3W9096 2.155 14.414 3.916 1.00 0.00 WT1 H -ATOM 771 H2 TIP3W9096 2.719 13.333 3.011 1.00 0.00 WT1 H -ATOM 772 OH2 TIP3W9226 8.578 0.832 6.351 1.00 0.00 WT1 O -ATOM 773 H1 TIP3W9226 7.928 0.530 5.693 1.00 0.00 WT1 H -ATOM 774 H2 TIP3W9226 8.563 1.801 6.335 1.00 0.00 WT1 H -ATOM 775 OH2 TIP3W9241 7.287 10.172 13.815 1.00 0.00 WT1 O -ATOM 776 H1 TIP3W9241 6.631 9.473 14.077 1.00 0.00 WT1 H -ATOM 777 H2 TIP3W9241 8.119 9.669 13.852 1.00 0.00 WT1 H -ATOM 778 OH2 TIP3W9250 3.347 10.487 19.814 1.00 0.00 WT1 O -ATOM 779 H1 TIP3W9250 2.792 10.955 19.188 1.00 0.00 WT1 H -ATOM 780 H2 TIP3W9250 4.264 10.639 19.456 1.00 0.00 WT1 H -END diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt deleted file mode 100644 index 2b550b6309..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt deleted file mode 100644 index 274d8aeb11..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt +++ /dev/null @@ -1,16 +0,0 @@ -import "spce.lt" - -wat = new SPCE [260] - - - - - - - -# Open up the PDB file to count the number of water molecules inside. (Or just -# divide the number of atoms by 3). Put that in between the brackets ("[260]") -# -# The command above does not set the positions of the atoms. -# So they will have to be loaded later from a PDB or an XYZ file. -# (For example, using "moltemplate.sh -pdb solvate.pdb system.lt") diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt deleted file mode 100644 index 4cbf67fc2d..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt +++ /dev/null @@ -1,49 +0,0 @@ -################################################## -# Box of water -################################################## -# -# define the system being simulated: - -# ----- init section ----- - -include system.in.init - - -# ----- atom definition section ----- - -read_data system.data - - -# ----- settings section ----- - -include system.in.settings - -# Load the atom coordinates: - -include "system.in.coords" - -# ----- run section ----- - - -# -- minimization protocol -- -# In general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 2.0 - -dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0 - -thermo_style custom step temp pe etotal press vol epair ebond eangle edihed -thermo 100 - -run 20000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt deleted file mode 100644 index ed2d026c4f..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt +++ /dev/null @@ -1,67 +0,0 @@ -################################################## -# Box of water -################################################## -# -# define the system being simulated: - -# -- init section -- -include system.in.init - -# ------------------------ Atom Definition Section -------------- - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Otherwise try "read_dump", "dump2data.py", or "restart2data". - -read_data system.data - -# ------------------------ Settings section --------------------- - -include system.in.settings - -# Load the atom coordinates: - -include "system.in.coords" - -# ------------------------ Run section ------------------------- - - -# -- minimization protocol -- - -# In general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 2.0 - -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - -thermo_style custom step temp pe etotal press vol epair ebond eangle -thermo 500 # time interval for printing out "thermo" data -#thermo_modify flush yes - -restart 100000 restart_nvt - -run 50000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh deleted file mode 100755 index cf51fa8705..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh +++ /dev/null @@ -1,33 +0,0 @@ -# --- Running LAMMPS --- -# -- Prerequisites: -- -# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files -# you hopefully have created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data -# If not, carry out the instructions in "README_setup.sh". -# -# -- Instructions: -- -# If "lmp_linux" is the name of the command you use to invoke lammps, -# then you would run lammps on these files this way: - - -lmp_linux -i run.in.npt # minimization and simulation at constant pressure - -# or - -lmp_linux -i run.in.nvt # minimization and simulation at constant volume - -#(Note: The constant volume simulation lacks pressure equilibration. These are -# completely separate simulations. The results of the constant pressure -# simulation are ignored when beginning the simulation at constant volume. -# This can be fixed. Read "run.in.nvt" for equilibration instructions.) - - - - - -# If you have compiled the MPI version of lammps, you can run lammps in parallel -#mpirun -np 4 lmp_linux -i run.in.npt -# or -#mpirun -np 4 lmp_linux -i run.in.nvt -# (assuming you have 4 processors available) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh deleted file mode 100755 index 3a08212692..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg deleted file mode 100644 index 5261bedc2c..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Cl.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg deleted file mode 100644 index 78c4056f8c..0000000000 Binary files a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/Na.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index d255bf3683..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,4257 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 3016 !NATOM - 1 1 3 3 -0.847600 15.9994 0 - 2 1 4 4 0.423800 1.0080 0 - 3 1 4 4 0.423800 1.0080 0 - 4 2 3 3 -0.847600 15.9994 0 - 5 2 4 4 0.423800 1.0080 0 - 6 2 4 4 0.423800 1.0080 0 - 7 3 3 3 -0.847600 15.9994 0 - 8 3 4 4 0.423800 1.0080 0 - 9 3 4 4 0.423800 1.0080 0 - 10 4 3 3 -0.847600 15.9994 0 - 11 4 4 4 0.423800 1.0080 0 - 12 4 4 4 0.423800 1.0080 0 - 13 5 3 3 -0.847600 15.9994 0 - 14 5 4 4 0.423800 1.0080 0 - 15 5 4 4 0.423800 1.0080 0 - 16 6 3 3 -0.847600 15.9994 0 - 17 6 4 4 0.423800 1.0080 0 - 18 6 4 4 0.423800 1.0080 0 - 19 7 3 3 -0.847600 15.9994 0 - 20 7 4 4 0.423800 1.0080 0 - 21 7 4 4 0.423800 1.0080 0 - 22 8 3 3 -0.847600 15.9994 0 - 23 8 4 4 0.423800 1.0080 0 - 24 8 4 4 0.423800 1.0080 0 - 25 9 3 3 -0.847600 15.9994 0 - 26 9 4 4 0.423800 1.0080 0 - 27 9 4 4 0.423800 1.0080 0 - 28 10 3 3 -0.847600 15.9994 0 - 29 10 4 4 0.423800 1.0080 0 - 30 10 4 4 0.423800 1.0080 0 - 31 11 3 3 -0.847600 15.9994 0 - 32 11 4 4 0.423800 1.0080 0 - 33 11 4 4 0.423800 1.0080 0 - 34 12 3 3 -0.847600 15.9994 0 - 35 12 4 4 0.423800 1.0080 0 - 36 12 4 4 0.423800 1.0080 0 - 37 13 3 3 -0.847600 15.9994 0 - 38 13 4 4 0.423800 1.0080 0 - 39 13 4 4 0.423800 1.0080 0 - 40 14 3 3 -0.847600 15.9994 0 - 41 14 4 4 0.423800 1.0080 0 - 42 14 4 4 0.423800 1.0080 0 - 43 15 3 3 -0.847600 15.9994 0 - 44 15 4 4 0.423800 1.0080 0 - 45 15 4 4 0.423800 1.0080 0 - 46 16 3 3 -0.847600 15.9994 0 - 47 16 4 4 0.423800 1.0080 0 - 48 16 4 4 0.423800 1.0080 0 - 49 17 3 3 -0.847600 15.9994 0 - 50 17 4 4 0.423800 1.0080 0 - 51 17 4 4 0.423800 1.0080 0 - 52 18 3 3 -0.847600 15.9994 0 - 53 18 4 4 0.423800 1.0080 0 - 54 18 4 4 0.423800 1.0080 0 - 55 19 3 3 -0.847600 15.9994 0 - 56 19 4 4 0.423800 1.0080 0 - 57 19 4 4 0.423800 1.0080 0 - 58 20 3 3 -0.847600 15.9994 0 - 59 20 4 4 0.423800 1.0080 0 - 60 20 4 4 0.423800 1.0080 0 - 61 21 3 3 -0.847600 15.9994 0 - 62 21 4 4 0.423800 1.0080 0 - 63 21 4 4 0.423800 1.0080 0 - 64 22 3 3 -0.847600 15.9994 0 - 65 22 4 4 0.423800 1.0080 0 - 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- -# Note: Monovalent ion parameters for Ewald and SPC/E water -# are from: Joung & Cheatham JPCB (2008) -# These Lennard Jones parameters match the parameters for ions -# in SPC/E water in the "frcmod.ionsjc_spce" file distributed -# with Amber (the 2010 version). - - -NaIon { - write_once("In Settings") { - pair_coeff @atom:Na @atom:Na lj/charmm/coul/long 0.3526418 1.212 - } - - write_once("Data Masses") { - @atom:Na 22.9898 - } - - # assumes "full" atom style - write("Data Atoms") { - $atom:Na $mol @atom:Na 1.0 0.00000 0.00000 0.000000 - } -} # NaIon - - -ClIon { - write_once("In Settings") { - pair_coeff @atom:Cl @atom:Cl lj/charmm/coul/long 0.0127850 2.711 - } - - write_once("Data Masses") { - @atom:Cl 35.453 - } - - # assumes "full" atom style - write("Data Atoms") { - $atom:Cl $mol @atom:Cl -1.0 0.00000 0.00000 0.000000 - } -} # ClIon - - -write_once("In Init") { - # -- Default styles for ions -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - kspace_style pppm 0.0001 - pair_modify mix arithmetic -} - -# Optional: Define a group named "ions" consisting of either Na or Cl ions. -write_once("In Settings") { - group ionNa type @atom:NaIon/Na @atom:NaIon/Na - group ionCl type @atom:ClIon/Cl @atom:ClIon/Cl - group ions type @atom:NaIon/Na @atom:ClIon/Cl -} - diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt deleted file mode 100644 index 2b550b6309..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/spce.lt +++ /dev/null @@ -1,52 +0,0 @@ -# file "spce.lt" -# -# H1 H2 -# \ / -# O - -SPCE { - - write_once("In Init") { - # -- Default styles (for solo "SPCE" water) -- - units real - atom_style full - # (Hybrid force fields were not necessary but are used for portability.) - pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 - bond_style hybrid harmonic - angle_style hybrid harmonic - kspace_style pppm 0.0001 - pair_modify mix arithmetic - } - - write("Data Atoms") { - $atom:O $mol:. @atom:O -0.8476 0.0000000 0.00000 0.000000 - $atom:H1 $mol:. @atom:H 0.4238 0.8164904 0.00000 0.5773590 - $atom:H2 $mol:. @atom:H 0.4238 -0.8164904 0.00000 0.5773590 - } - - write_once("Data Masses") { - @atom:O 15.9994 - @atom:H 1.008 - } - - write("Data Bonds") { - $bond:OH1 @bond:OH $atom:O $atom:H1 - $bond:OH2 @bond:OH $atom:O $atom:H2 - } - - write("Data Angles") { - $angle:HOH @angle:HOH $atom:H1 $atom:O $atom:H2 - } - - write_once("In Settings") { - bond_coeff @bond:OH harmonic 1000.0 1.0 - angle_coeff @angle:HOH harmonic 1000.0 109.47 - pair_coeff @atom:O @atom:O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @atom:H @atom:H lj/charmm/coul/long 0.0 2.058 - group spce type @atom:O @atom:H - fix fSHAKE spce shake 0.0001 10 100 b @bond:OH a @angle:HOH - # (Remember to "unfix" fSHAKE during minimization.) - } - -} # end of definition of "SPCE" water molecule type - diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt deleted file mode 100644 index f43f4263e8..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt +++ /dev/null @@ -1,52 +0,0 @@ -import "spce.lt" # <- This defines the SPCE water molecule. This file is - # located in the "common" directory. You can either copy it - # here, or (preferably), you can define a MOLTEMPLATE_PATH - # environment variable and point it to "common". - # (as explained in the installation section of the manual). - -import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". - -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 34.50 xlo xhi - 0.0 34.50 ylo yhi - 0.0 34.50 zlo zhi -} - - -# The next command generates a (rather dense) cubic lattice with -# spacing 3.45 Angstroms. (The pressure must be equilibrated later.) - -wat = new SPCE [10].move(0.00, 0.00, 3.45) - [10].move(0.00, 3.45, 0.00) - [10].move(3.45, 0.00, 0.00) - -# We now create a 2x2x2 lattice of Na+ and Cl- ions: - -na = new NaIon [2].move(0,0,17.25) - [2].move(0,17.25,0) - [2].move(17.25,0,0) - - -cl = new ClIon [2].move(0,0,17.25) - [2].move(0,17.25,0) - [2].move(17.25,0,0) - -na[*][*][*].move(5.175,5.175,5.6) -cl[*][*][*].move(12.075,12.075,12.5) - -# (The (5.175,5.175,5.175) and (12.075,12.075,12.075) translational shifts -# prevent the Na and Cl ions from overlapping -# with the water molecules or each other.) - - -# Comment: Fortunately the ions and the water in this example share the -# same force-field styles (so their was no need to use "hybrid" styles). -# If this were not the case, you might need to add something like this. -# -# write_once("In Init") { -# # -- Styles for the combined system (overrides earlier settings) -- -# pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0 NEWPAIRSTYLE -# bond_style hybrid harmonic NEWBONDSTYLE -# angle_style hybrid harmonic NEWANGLESTYLE -# } diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt deleted file mode 100644 index b129469a88..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt +++ /dev/null @@ -1,38 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - -timestep 2.0 -dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz -fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 - -thermo 100 -#thermo_modify flush yes - -run 20000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt deleted file mode 100644 index b23a288c47..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt +++ /dev/null @@ -1,61 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - - -# Normally, I would minimize the system and equilibrate the system at constant -# pressure and temperature beforehand. If you run lammps with "run.in.npt", -# it will generate a restart file "system_after_npt.rst" with reasonable -# coordinates at that temperature and pressure. Then we could load it now: -# -#read_restart system_after_npt.rst -# -# Unfortunately the LAMMPS "read_restart" command has been undependable over -# the past year (2012), and I feel it is safer to remove it from the examples. -# Instead, for this example, I just read the raw coordinates generated by -# moltemplate (and the default volume). (I get fewer questions this way.) -# However you should never run any liquid simulations at constant volume without -# pressure equilibration first. Hopefully in the future "read_restart" will -# work. Until then, try "read_dump", "dump2data.py", or "restart2data". - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -# -- minimization protocol -- - -# Note: The minimization step is not necessary in this example. However -# in general, it's always a good idea to minimize the system beforehand. -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 -# Now read "system.in.settings" in order to redefine fSHAKE again: -include system.in.settings - -# -- simulation protocol -- - - - -timestep 2.0 -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 - - -thermo 500 -#thermo_modify flush yes - - -#restart 100000 restart_nvt - -run 50000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT deleted file mode 100644 index 76caac02cc..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README.TXT +++ /dev/null @@ -1,22 +0,0 @@ - Description: - -This is a simulation of pyramid-shaped objects resting on an immobile surface -(resembling graphene). Each pyramid is built from spherical particles stacked -like cannon-balls, or stacked fruit. Ordinarily, the stack does not move -because the particles at the ground layer are immobilized. However, -given an initial (small) perturbation the pyramids collapse in an avalanche. - -(In this example, the perturbation is due to shock because we (intentionally) - did not minimize the system before starting the simulation. This shock - causes an avalanche to occur approximately 5000 timesteps later.) - -The particles roll down the pyramid and bounce off the "ground". The bouncing -is due to a repulsive external force which is added artificially. -(See the "run.in" file.) The simulation looks weird without something -to bounce off of. So I added a graphene surface at the bottom as scenery. -(It does not exert any force on the atoms.) - -(Random comment: This could be a fun example to illustrate the Boltzmann - distribution. Because there is no damping, in a small region, the particle - heights should eventually approach the Boltzmann distribution for some - suitable temperature.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt deleted file mode 100644 index 096674f7ff..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_VMD_graphene.txt +++ /dev/null @@ -1,28 +0,0 @@ - ------- A note on building the graphene sheet in VMD: ------ - -Probably you can ignore these instructions. -These instructions are not necessary for this example to run. - -This example contains several pyramid shaped objects resting on a surface -made of graphene. The instructions in this file explain how to build the -graphene (representing the "ground") using VMD instead of with moltemplate. - Why do this? -VMD can create graphene sheets with bonds connecting neighboring carbon atoms, -(which looks more pretty). However, as of 2013-4-29, moltemplate currently -can not generate these bonds. It does not matter physically in this case, -because the graphene sheet used here does not move. It is only used as -scenery, to graphically represent the ground surface. - -Select "Extensions"->"Modeling"->"Carbon Nanotube Builder" - Build a graphene sheet of size 39.8 x 39.8 (units: nm) - 400.3358398 399.876008 - (try to use a size compatible with the periodic boundaries) -Select "Extensions"->"Tk Console", and type - display backgroundgradient on - -Note: If you want to do this, before you run moltemplate, you may want to delete - the sections of the "system.lt" file (located in "moltemplate_files") - which define the graphene wall. Instead create the graphene data file - in VMD. You will have to manually merge the data file for graphene - with the data file for the pyramids created by moltemplate, - (taking care to avoid overlapping atom-id numbers). diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_setup.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt deleted file mode 100644 index 10198fc92f..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/README_visualize.txt +++ /dev/null @@ -1,76 +0,0 @@ - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - To shift the box by a fraction in the x direction (for example) - do this: - - pbc wrap -compound res -all -shiftcenterrel {-0.50 -0.52 0.0 } - pbc box -shiftcenterrel {-0.50 -0.52 0.0 } - - # Alternately if you have a solute whose atoms are all of type 1, - # then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg deleted file mode 100644 index dc010258f0..0000000000 Binary files a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=04800steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg deleted file mode 100644 index 53dc98f3e8..0000000000 Binary files a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=12200steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg b/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg deleted file mode 100644 index ba07b25372..0000000000 Binary files a/tools/moltemplate/examples/silly/pyramids_vs_gravity/images/pyramids_vs_gravity_t=33000steps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh deleted file mode 100644 index 365ab9fb03..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/README.sh +++ /dev/null @@ -1,15 +0,0 @@ -# This directory contains moltemplate files for the "Pyramids of Giza" example. -# (Note: the ground lattice work that appears in some images was not generated -# by moltemplate. Moltemplate can not currently create bonded periodic -# structures as of 2013-4-04. Those were generated by topotools.) -# -# To run moltemplate, use: - -moltemplate.sh system.lt - -# This will generate:system.data, system.in, system.in.init, system.in.settings -# -# The output_ttree/ directory will contain files like "Data Atoms", "Data Bonds" -# which contain the corresponding structures of the system.data file. -# (This might make it slightly easier to combine them with atom data and -# bond data generated by other programs, such as topotools, for example.) diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt deleted file mode 100644 index 3b3e21333f..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene.lt +++ /dev/null @@ -1,61 +0,0 @@ -# This file contains a unit cell for building graphene and nanotubes -# -# -# The 4AtomRectCellXY "molecule" defined below is a reactangular unit cell -# for hexagonal tesselations in 2-dimensions. (See "graphene_unit_cell.jpg") -# Surfaces constructed with this unit cell can be flat or curved into tubes. -# The distance between nearest-neighbor carbon atoms (ie the length of a -# carbon-carbon bond) is equal to "d" which I set to 1.42 Angstroms. -# -# d = length of each hexagon's side = 1.42 Angstroms -# L = length of each hexagon = 2*d = 2.84 Angstroms -# W = width of each hexagon = 2*d*sqrt(3)/2 = 2.4595121467478056 Angstroms -# 2w = width of hexagon rows = 3*l = 4.26 Angstroms -# -# Consequently, the Lattice-cell vectors for singe-layer graphene are: -# (2.4595121467478, 0, 0) (aligned with X axis) -# (0, 4.26, 0) (aligned with Y axis) -# So, to build a sheet of graphite, you could use: -# sheet = new Graphene/4AtomRectCellXY [10].move(2.4595121467478, 0, 0) -# [10].move(0, 4.26, 0) - - - - -Graphene { - - 4AtomRectCellXY - { - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom:C11 $mol:... @atom:../C 0.0 0.61487803668695 0.71 0.0 - $atom:C21 $mol:... @atom:../C 0.0 1.84463411006085 1.42 0.0 - $atom:C12 $mol:... @atom:../C 0.0 0.61487803668695 3.55 0.0 - $atom:C22 $mol:... @atom:../C 0.0 1.84463411006085 2.84 0.0 - } - } - - # Now define properties of the Carbon graphene atom - - write_once("In Init") { - pair_style hybrid lj/cut 9.0 - } - - write_once("Data Masses") { - @atom:C 12.0 - } - - write_once("In Settings") { - # i j epsilon sigma - pair_coeff @atom:C @atom:C lj/cut 0.068443 3.407 - - # These Lennard-Jones parameters come from - # R. Saito, R. Matsuo, T. Kimura, G. Dresselhaus, M.S. Dresselhaus, - # Chem Phys Lett, 348:187 (2001) - - # Define a group consisting of only carbon atoms in graphene molecules - group gGraphene type @atom:C - } - -} # Graphene - diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt deleted file mode 100644 index 759f0f5d06..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/graphene_wall.lt +++ /dev/null @@ -1,21 +0,0 @@ -import "graphene.lt" - -# -------------- graphene sheet ----------------- - -# Notes: -# Hexagonal lattice with: -# l = length of each hexagonal side = 1.42 Angstroms -# L = length of each hexagon = 2*l = 2.84 Angstroms -# W = width of each hexagon = 2*l*sqrt(3)/2 ~= 2.4595121467478 Angstroms -# 2w = width of hexagon rows = 3.0*l = 4.26 Angstroms - - -GrapheneWall { - - unitcells = new Graphene/4AtomRectCellXY [163].move(2.456, 0, 0) - [94].move(0, 4.254, 0) - - # (Note: I fudged the spacing slightly to make it line up better with the - # lattice spacing for graphene generated by VMD's graphene builder.) -} - diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt deleted file mode 100644 index 7585b4ce0c..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/pyramids.lt +++ /dev/null @@ -1,290 +0,0 @@ -# Brick is a very simple molecule containing one "atom". -# "ImmobileBrick" and "GoldBrick" are identical to "Brick" but are -# given different atom types. (This makes it easier to put them in -# different groups and apply different LAMMPS "fixes" to them.) - -Brick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gMobile type @atom - # (Atoms of this type belong to the "gMobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style lj/cut 1.0 - } -} - - - -#We want to stack "Brick"s the same way a green-grocer sometimes stack apples: -#Place the apples at the base an square lattice of apples at the base. -#The apples in the next layer up are placed in between the 4 apples beneath them. -#Each new layer is smaller and placed above the previous layer at a height -#of sigma / sqrt(2), where "sigma" is the diameter of each spherical "Brick". -#We will artificially hold the apples at the base in place -#(to keep the entire stack from collapsing). -# -# The lines below were generated from the following python loop: -# -#from math import * -#N=50 -#s=1.0 -#for i in range(0,N): -# print(" layer"+str(i)+" = new Brick.move("+str(-(N-(i+1))*s*0.5)+","+ -# str(-(N-(i+1))*s*0.5)+","+str(i*s/sqrt(2))+") ["+str(N-i)+"].move("+ -# str(s)+",0,0) ["+str(N-i)+"].move(0,"+str(s)+",0)") - - -PyramidKhufu { - layer0 = new ImmobileBrick.move(-24.5,-24.5,0.0) [50].move(1.0,0,0) [50].move(0,1.0,0) - layer1 = new Brick.move(-24.0,-24.0,0.707106781187) [49].move(1.0,0,0) [49].move(0,1.0,0) - layer2 = new Brick.move(-23.5,-23.5,1.41421356237) [48].move(1.0,0,0) [48].move(0,1.0,0) - layer3 = new Brick.move(-23.0,-23.0,2.12132034356) [47].move(1.0,0,0) [47].move(0,1.0,0) - layer4 = new Brick.move(-22.5,-22.5,2.82842712475) [46].move(1.0,0,0) [46].move(0,1.0,0) - layer5 = new Brick.move(-22.0,-22.0,3.53553390593) [45].move(1.0,0,0) [45].move(0,1.0,0) - layer6 = new Brick.move(-21.5,-21.5,4.24264068712) [44].move(1.0,0,0) [44].move(0,1.0,0) - layer7 = new Brick.move(-21.0,-21.0,4.94974746831) [43].move(1.0,0,0) [43].move(0,1.0,0) - layer8 = new Brick.move(-20.5,-20.5,5.65685424949) [42].move(1.0,0,0) [42].move(0,1.0,0) - layer9 = new Brick.move(-20.0,-20.0,6.36396103068) [41].move(1.0,0,0) [41].move(0,1.0,0) - layer10 = new Brick.move(-19.5,-19.5,7.07106781187) [40].move(1.0,0,0) [40].move(0,1.0,0) - layer11 = new Brick.move(-19.0,-19.0,7.77817459305) [39].move(1.0,0,0) [39].move(0,1.0,0) - layer12 = new Brick.move(-18.5,-18.5,8.48528137424) [38].move(1.0,0,0) [38].move(0,1.0,0) - layer13 = new Brick.move(-18.0,-18.0,9.19238815543) [37].move(1.0,0,0) [37].move(0,1.0,0) - layer14 = new Brick.move(-17.5,-17.5,9.89949493661) [36].move(1.0,0,0) [36].move(0,1.0,0) - layer15 = new Brick.move(-17.0,-17.0,10.6066017178) [35].move(1.0,0,0) [35].move(0,1.0,0) - layer16 = new Brick.move(-16.5,-16.5,11.313708499) [34].move(1.0,0,0) [34].move(0,1.0,0) - layer17 = new Brick.move(-16.0,-16.0,12.0208152802) [33].move(1.0,0,0) [33].move(0,1.0,0) - layer18 = new Brick.move(-15.5,-15.5,12.7279220614) [32].move(1.0,0,0) [32].move(0,1.0,0) - layer19 = new Brick.move(-15.0,-15.0,13.4350288425) [31].move(1.0,0,0) [31].move(0,1.0,0) - layer20 = new Brick.move(-14.5,-14.5,14.1421356237) [30].move(1.0,0,0) [30].move(0,1.0,0) - layer21 = new Brick.move(-14.0,-14.0,14.8492424049) [29].move(1.0,0,0) [29].move(0,1.0,0) - layer22 = new Brick.move(-13.5,-13.5,15.5563491861) [28].move(1.0,0,0) [28].move(0,1.0,0) - layer23 = new Brick.move(-13.0,-13.0,16.2634559673) [27].move(1.0,0,0) [27].move(0,1.0,0) - layer24 = new Brick.move(-12.5,-12.5,16.9705627485) [26].move(1.0,0,0) [26].move(0,1.0,0) - layer25 = new Brick.move(-12.0,-12.0,17.6776695297) [25].move(1.0,0,0) [25].move(0,1.0,0) - layer26 = new Brick.move(-11.5,-11.5,18.3847763109) [24].move(1.0,0,0) [24].move(0,1.0,0) - layer27 = new Brick.move(-11.0,-11.0,19.091883092) [23].move(1.0,0,0) [23].move(0,1.0,0) - layer28 = new Brick.move(-10.5,-10.5,19.7989898732) [22].move(1.0,0,0) [22].move(0,1.0,0) - layer29 = new Brick.move(-10.0,-10.0,20.5060966544) [21].move(1.0,0,0) [21].move(0,1.0,0) - layer30 = new Brick.move(-9.5,-9.5,21.2132034356) [20].move(1.0,0,0) [20].move(0,1.0,0) - layer31 = new Brick.move(-9.0,-9.0,21.9203102168) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer32 = new Brick.move(-8.5,-8.5,22.627416998) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer33 = new Brick.move(-8.0,-8.0,23.3345237792) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer34 = new Brick.move(-7.5,-7.5,24.0416305603) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer35 = new Brick.move(-7.0,-7.0,24.7487373415) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer36 = new Brick.move(-6.5,-6.5,25.4558441227) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer37 = new Brick.move(-6.0,-6.0,26.1629509039) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer38 = new Brick.move(-5.5,-5.5,26.8700576851) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer39 = new Brick.move(-5.0,-5.0,27.5771644663) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer40 = new GoldBrick.move(-4.5,-4.5,28.2842712475) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer41 = new GoldBrick.move(-4.0,-4.0,28.9913780286) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer42 = new GoldBrick.move(-3.5,-3.5,29.6984848098) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer43 = new GoldBrick.move(-3.0,-3.0,30.405591591) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer44 = new GoldBrick.move(-2.5,-2.5,31.1126983722) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer45 = new GoldBrick.move(-2.0,-2.0,31.8198051534) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer46 = new GoldBrick.move(-1.5,-1.5,32.5269119346) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer47 = new GoldBrick.move(-1.0,-1.0,33.2340187158) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer48 = new GoldBrick.move(-0.5,-0.5,33.941125497) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer49 = new GoldBrick.move(0.0,0.0,34.6482322781) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - -PyramidKhafre { - layer0 = new ImmobileBrick.move(-23.5,-23.5,0.0) [48].move(1.0,0,0) [48].move(0,1.0,0) - layer1 = new Brick.move(-23.0,-23.0,0.707106781187) [47].move(1.0,0,0) [47].move(0,1.0,0) - layer2 = new Brick.move(-22.5,-22.5,1.41421356237) [46].move(1.0,0,0) [46].move(0,1.0,0) - layer3 = new Brick.move(-22.0,-22.0,2.12132034356) [45].move(1.0,0,0) [45].move(0,1.0,0) - layer4 = new Brick.move(-21.5,-21.5,2.82842712475) [44].move(1.0,0,0) [44].move(0,1.0,0) - layer5 = new Brick.move(-21.0,-21.0,3.53553390593) [43].move(1.0,0,0) [43].move(0,1.0,0) - layer6 = new Brick.move(-20.5,-20.5,4.24264068712) [42].move(1.0,0,0) [42].move(0,1.0,0) - layer7 = new Brick.move(-20.0,-20.0,4.94974746831) [41].move(1.0,0,0) [41].move(0,1.0,0) - layer8 = new Brick.move(-19.5,-19.5,5.65685424949) [40].move(1.0,0,0) [40].move(0,1.0,0) - layer9 = new Brick.move(-19.0,-19.0,6.36396103068) [39].move(1.0,0,0) [39].move(0,1.0,0) - layer10 = new Brick.move(-18.5,-18.5,7.07106781187) [38].move(1.0,0,0) [38].move(0,1.0,0) - layer11 = new Brick.move(-18.0,-18.0,7.77817459305) [37].move(1.0,0,0) [37].move(0,1.0,0) - layer12 = new Brick.move(-17.5,-17.5,8.48528137424) [36].move(1.0,0,0) [36].move(0,1.0,0) - layer13 = new Brick.move(-17.0,-17.0,9.19238815543) [35].move(1.0,0,0) [35].move(0,1.0,0) - layer14 = new Brick.move(-16.5,-16.5,9.89949493661) [34].move(1.0,0,0) [34].move(0,1.0,0) - layer15 = new Brick.move(-16.0,-16.0,10.6066017178) [33].move(1.0,0,0) [33].move(0,1.0,0) - layer16 = new Brick.move(-15.5,-15.5,11.313708499) [32].move(1.0,0,0) [32].move(0,1.0,0) - layer17 = new Brick.move(-15.0,-15.0,12.0208152802) [31].move(1.0,0,0) [31].move(0,1.0,0) - layer18 = new Brick.move(-14.5,-14.5,12.7279220614) [30].move(1.0,0,0) [30].move(0,1.0,0) - layer19 = new Brick.move(-14.0,-14.0,13.4350288425) [29].move(1.0,0,0) [29].move(0,1.0,0) - layer20 = new Brick.move(-13.5,-13.5,14.1421356237) [28].move(1.0,0,0) [28].move(0,1.0,0) - layer21 = new Brick.move(-13.0,-13.0,14.8492424049) [27].move(1.0,0,0) [27].move(0,1.0,0) - layer22 = new Brick.move(-12.5,-12.5,15.5563491861) [26].move(1.0,0,0) [26].move(0,1.0,0) - layer23 = new Brick.move(-12.0,-12.0,16.2634559673) [25].move(1.0,0,0) [25].move(0,1.0,0) - layer24 = new Brick.move(-11.5,-11.5,16.9705627485) [24].move(1.0,0,0) [24].move(0,1.0,0) - layer25 = new Brick.move(-11.0,-11.0,17.6776695297) [23].move(1.0,0,0) [23].move(0,1.0,0) - layer26 = new Brick.move(-10.5,-10.5,18.3847763109) [22].move(1.0,0,0) [22].move(0,1.0,0) - layer27 = new Brick.move(-10.0,-10.0,19.091883092) [21].move(1.0,0,0) [21].move(0,1.0,0) - layer28 = new Brick.move(-9.5,-9.5,19.7989898732) [20].move(1.0,0,0) [20].move(0,1.0,0) - layer29 = new Brick.move(-9.0,-9.0,20.5060966544) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer30 = new Brick.move(-8.5,-8.5,21.2132034356) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer31 = new Brick.move(-8.0,-8.0,21.9203102168) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer32 = new Brick.move(-7.5,-7.5,22.627416998) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer33 = new Brick.move(-7.0,-7.0,23.3345237792) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer34 = new Brick.move(-6.5,-6.5,24.0416305603) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer35 = new GoldBrick.move(-6.0,-6.0,24.7487373415) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer36 = new GoldBrick.move(-5.5,-5.5,25.4558441227) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer37 = new GoldBrick.move(-5.0,-5.0,26.1629509039) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer38 = new GoldBrick.move(-4.5,-4.5,26.8700576851) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer39 = new GoldBrick.move(-4.0,-4.0,27.5771644663) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer40 = new GoldBrick.move(-3.5,-3.5,28.2842712475) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer41 = new GoldBrick.move(-3.0,-3.0,28.9913780286) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer42 = new GoldBrick.move(-2.5,-2.5,29.6984848098) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer43 = new GoldBrick.move(-2.0,-2.0,30.405591591) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer44 = new GoldBrick.move(-1.5,-1.5,31.1126983722) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer45 = new GoldBrick.move(-1.0,-1.0,31.8198051534) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer46 = new GoldBrick.move(-0.5,-0.5,32.5269119346) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer47 = new GoldBrick.move(0.0,0.0,33.2340187158) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - -PyramidMenkaure { - layer0 = new ImmobileBrick.move(-9.0,-9.0,0.0) [19].move(1.0,0,0) [19].move(0,1.0,0) - layer1 = new Brick.move(-8.5,-8.5,0.707106781187) [18].move(1.0,0,0) [18].move(0,1.0,0) - layer2 = new Brick.move(-8.0,-8.0,1.41421356237) [17].move(1.0,0,0) [17].move(0,1.0,0) - layer3 = new Brick.move(-7.5,-7.5,2.12132034356) [16].move(1.0,0,0) [16].move(0,1.0,0) - layer4 = new Brick.move(-7.0,-7.0,2.82842712475) [15].move(1.0,0,0) [15].move(0,1.0,0) - layer5 = new Brick.move(-6.5,-6.5,3.53553390593) [14].move(1.0,0,0) [14].move(0,1.0,0) - layer6 = new Brick.move(-6.0,-6.0,4.24264068712) [13].move(1.0,0,0) [13].move(0,1.0,0) - layer7 = new Brick.move(-5.5,-5.5,4.94974746831) [12].move(1.0,0,0) [12].move(0,1.0,0) - layer8 = new Brick.move(-5.0,-5.0,5.65685424949) [11].move(1.0,0,0) [11].move(0,1.0,0) - layer9 = new Brick.move(-4.5,-4.5,6.36396103068) [10].move(1.0,0,0) [10].move(0,1.0,0) - layer10 = new Brick.move(-4.0,-4.0,7.07106781187) [9].move(1.0,0,0) [9].move(0,1.0,0) - layer11 = new Brick.move(-3.5,-3.5,7.77817459305) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer12 = new Brick.move(-3.0,-3.0,8.48528137424) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer13 = new Brick.move(-2.5,-2.5,9.19238815543) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer14 = new Brick.move(-2.0,-2.0,9.89949493661) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer15 = new Brick.move(-1.5,-1.5,10.6066017178) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer16 = new Brick.move(-1.0,-1.0,11.313708499) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer17 = new Brick.move(-0.5,-0.5,12.0208152802) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer18 = new Brick.move(0.0,0.0,12.7279220614) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens1 { - #layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - #layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - #layer2 = new ImmobileBrick.move(-2.0,-2.0,1.41421356237) [5].move(1.0,0,0) [5].move(0,1.0,0) - #layer3 = new ImmobileBrick.move(-1.5,-1.5,2.12132034356) [4].move(1.0,0,0) [4].move(0,1.0,0) - #layer4 = new Brick.move(-0.5,-0.5,2.82842712475) [2].move(1.0,0,0) [2].move(0,1.0,0) - #layer5 = new Brick.move(0.0,0.0,3.53553390593) [1].move(1.0,0,0) [1].move(0,1.0,0) - - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens2 { - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new ImmobileBrick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new ImmobileBrick.move(-2.0,-2.0,1.707106781187) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer3 = new Brick.move(-1.5,-1.5,2.41421356237) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer4 = new Brick.move(-0.5,-0.5,3.41421356237) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer5 = new Brick.move(0.0,0.0,4.12132034356) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - -PyramidQueens3 { - layer0 = new ImmobileBrick.move(-3.5,-3.5,0.0) [8].move(1.0,0,0) [8].move(0,1.0,0) - layer1 = new Brick.move(-3.0,-3.0,0.707106781187) [7].move(1.0,0,0) [7].move(0,1.0,0) - layer2 = new Brick.move(-2.5,-2.5,1.41421356237) [6].move(1.0,0,0) [6].move(0,1.0,0) - layer3 = new Brick.move(-2.0,-2.0,2.12132034356) [5].move(1.0,0,0) [5].move(0,1.0,0) - layer4 = new Brick.move(-1.5,-1.5,2.82842712475) [4].move(1.0,0,0) [4].move(0,1.0,0) - layer5 = new Brick.move(-1.0,-1.0,3.53553390593) [3].move(1.0,0,0) [3].move(0,1.0,0) - layer6 = new Brick.move(-0.5,-0.5,4.24264068712) [2].move(1.0,0,0) [2].move(0,1.0,0) - layer7 = new Brick.move(0.0,0.0,4.94974746831) [1].move(1.0,0,0) [1].move(0,1.0,0) -} - - - - -# "ImmobileBrick"s are identical to "Brick"s, -# except that they have a different atom type. -# We can define groups based on atom type -# and apply fixes to them. - -ImmobileBrick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gImmobile type @atom - # (Atoms of this type belong to the "gImmobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style hybrid lj/cut 1.0 - } -} - - - -GoldBrick { - - # atomID molID atomType charge x y z - write("Data Atoms") { - $atom $mol @atom 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom 1.0 - } - - write_once("In Settings") { - # U(r) = 4*epsilon_ij*((sigma_ij/r)^12 - (sigma_ij/r)^6) - # - # i j eps sig - pair_coeff @atom @atom lj/cut 1.0 0.8908987181403393 - } - - write_once("In Settings") { - group gMobile type @atom - # (Atoms of this type belong to the "gMobile" group) - } - - write_once("In Init") { - atom_style full - units lj - pair_style lj/cut 1.0 - } -} - diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt deleted file mode 100644 index 0c9c50ae9b..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/moltemplate_files/system.lt +++ /dev/null @@ -1,80 +0,0 @@ -# Description. -# This is a simulation of pyramid-like objects made of particles stacked -# and arranged like cannon-balls, or fruit-stands. Ordinarilly, the stack -# does not collapse because the particles at the ground layer are immobilized. -# However given an initial perterbation the pyramids collapse in an avalanche. -# (This can happen, for example when you do not minimize the system beforehand.) -# The particles roll down the pyramid and bounce off the "ground". The bouncing -# is due to a repulsive external force which is added artificially. -# (See the "run.in" file.) The simulation looks weird without something -# to bounce off of. So I added a graphene surface at the bottom as scenery. -# The ground does not serve any purpose except to look pretty. -# -# (Because there is no damping, I suspect that the distribution of heights of -# the particles in a small area should approach the Boltzmann distribution, -# if you run the simulation long enough.) - - -# ----------------- Pyramids: ----------------- - -import "pyramids.lt" - -# Move the pyramids into their locations in Giza (approximate) - -pyramidKhufu = new PyramidKhufu.move(210, 215, 1) -pyramidKhafre = new PyramidKhafre.move(150, 150, 1) -pyramidMenkaure = new PyramidMenkaure.move(105, 082, 1) -PyramidQueens1 = new PyramidQueens1.move(089, 059, 1) -PyramidQueens2 = new PyramidQueens2.move(100, 059, 1) -PyramidQueens3 = new PyramidQueens3.move(111, 059, 1) - - -# --------------- Scenery: -------------------- - -import "graphene_wall.lt" - -graphene_wall = new GrapheneWall - -write_once("In Settings") { - # Turn off all interactions with the graphene atoms by setting epsilon to 0. - # (We will use a different repulsive barrier to represent the ground instead.) - # These atoms are just "for show". epsilon sigma - pair_coeff @atom:Graphene/C @atom:Graphene/C lj/cut 0.00000 3.407 - - # Optional: Add the graphene atoms to the "gImmobile" group. Later freeze them - group gImmobile type @atom:Graphene/C -} - -# Unfortunately, the ground still looks kind of ugly because moltemplate does -# not yet know how to automatically connect nearby carbon atoms with C-C bonds -# (based on distance). (As of 2013-4-29, moltemplate is not good at -# generating crystalline objects containing explicit bonds.) -# If you want bonds between atoms, use VMD's "carbon-nanotube-builder plugin" -# (which creates data files with bonds) and then merge the two data files -# manually later. (This is not done here.) - - -# -------- override earlier settings ---------- - -write_once("In Init") { - # Override any earlier style settings - atom_style full - units lj - pair_style hybrid lj/cut 1.0 - bond_style none - angle_style none - dihedral_style none - improper_style none - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 0.0 -} - -# ------------ boundary conditions ------------ - -write_once("Data Boundary") { - -1.842033 398.493813 xlo xhi - -0.708994 399.167013 ylo yhi - 0.0 400.0 zlo zhi -} -# --------------------------------------------- - diff --git a/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in b/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in deleted file mode 100644 index 4feec9ff4e..0000000000 --- a/tools/moltemplate/examples/silly/pyramids_vs_gravity/run.in +++ /dev/null @@ -1,64 +0,0 @@ -# -- Init Section -- - -include system.in.init -boundary p p f - -# -- Atom Definition Section -- - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 0.0025 -dump 1 all custom 200 traj_nvt.lammpstrj id mol type x y z ix iy iz - -thermo_style custom step temp pe etotal -thermo 100 # time interval for printing out "thermo" data - -# ---- Set up the physical environment ---- - -# Add gravity: -fix fxGrav gMobile gravity 0.05 vector 0 0 -1 - -# Create a "ground" surface. -# This is a repulsive "wall" which particles can bounce off of: - -fix fxWall gMobile wall/lj126 zlo EDGE 1.0 0.8908987181403393 1.0 - - -# ---- Evolve the system: ---- - -# Evolve the (mobile) atoms using ordinary Newton's laws (NVE) - -fix fxNVE gMobile nve - - -# IF YOU WANT TO ADD DAMPING, THEN UNCOMMENT THE NEXT LINE: -#fix fxLan gMobile langevin 0.001 0.001 10000.0 48279 -# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve" -# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.) -# This was not tested. - -# For efficient simulation in parallel, try using "fix balance": -# (This will adjust the spatial decomposition as the distribution of -# particles changes over time.) - -fix fxBalance gMobile balance 1000 xy 20 1.3 - -# Optional: Improve efficiency by omitting the calcuation of interactions -# between immobile atoms: - -neigh_modify exclude group gImmobile gImmobile - - -restart 50000 restart_nvt - -run 200000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/silly/sierpinski/README.TXT b/tools/moltemplate/examples/silly/sierpinski/README.TXT deleted file mode 100644 index 6bc152b186..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/README.TXT +++ /dev/null @@ -1,45 +0,0 @@ -NOTE: This example requires the "Al99.eam.alloy" file. - (It was not included in this directory because if its large size.) - As of 2012-11, I was able to obtain it here: - http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - Copy it to the directory containing this README file. ------------------------------------------------------------------------- -3D fractal test - -Moltemplate is useful for building larger molecular structures from -smaller pieces. Although this simulation is of no scientific value, thiss -example illustrates how to build large (many-level) heirarchical objects -(Serpinski cubes) using moltemplate. (This is also called a "Menger Sponge".) - -The files in this directory demonstrate a way to build a periodic lattice of -3-dimensional Serpinski-cubes (with 3 levels of recursive self-similarity). - -In this example, the basic indivisible units are 4-atoms of Aluminum -(arranged in a cubic FCC unit-cell for bulk Aluminum). -This was an arbitrary choice. The resulting construct is not stable. -(But it makes pretty movies while collapsing.) - -To understand what is going on with this example, look at this file: - -./moltemplate_files/elegant_inefficient_version/serpinski_cubes.lt - -(This approach uses too much memory to be practical for large simulaions. -The version I actually use is here: ./moltemplate_files/serpinski_cubes.lt) - - --- To build the system --- - -Carry out the instructions in README_setup.sh, -to generate the LAMMPS DATA file and input scripts you need: -system.data, system.in.init, system.in.settings. -(The run.in script contains references to these files.) - - --- To run LAMMPS, try a command like: --- - -lmp_linux -i run.in - - or (if you have mpi installed) - -mpirun -np 4 lmp_linux -i run.in - -This will create an ordinary LAMMPS dump file you can visualize with VMD -traj.lammpstrj (See README_visualize.txt) diff --git a/tools/moltemplate/examples/silly/sierpinski/README_setup.sh b/tools/moltemplate/examples/silly/sierpinski/README_setup.sh deleted file mode 100755 index 2af3d7372c..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/README_setup.sh +++ /dev/null @@ -1,29 +0,0 @@ -# Use these commands to generate the LAMMPS input script and data file -# (and other auxilliary files): - - -# Create LAMMPS input files this way: -cd moltemplate_files - - # run moltemplate - - moltemplate.sh -atomstyle full system.lt - - # This will generate various files with names ending in *.in* and *.data. - # These files are the input files directly read by LAMMPS. Move them to - # the parent directory (or wherever you plan to run the simulation). - - mv -f system.in* system.data ../ - - # We will also need the "Al99.eam.alloy" file: - #cp -f Al99.eam.alloy ../ - # This file was downloaded from: - # http://www.ctcms.nist.gov/~cbecker/Download/Al-YM/Al99.eam.alloy - - - # Optional: - # The "./output_ttree/" directory is full of temporary files generated by - # moltemplate. They can be useful for debugging, but are usually thrown away. - rm -rf output_ttree/ - -cd ../ diff --git a/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt b/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/README_visualize.txt +++ /dev/null @@ -1,87 +0,0 @@ - - ------- To view a lammps trajectory in VMD -------- - - -1) Build a PSF file for use in viewing with VMD. - -This step works with VMD 1.9 and topotools 1.2. -(Older versions, like VMD 1.8.6, don't support this.) - - -a) Start VMD -b) Menu Extensions->Tk Console -c) Enter: - -(I assume that the the DATA file is called "system.data") - - topo readlammpsdata system.data full - animate write psf system.psf - -2) - -Later, to Load a trajectory in VMD: - - Start VMD - Select menu: File->New Molecule - -Browse to select the PSF file you created above, and load it. - (Don't close the window yet.) - -Browse to select the trajectory file. - If necessary, for "file type" select: "LAMMPS Trajectory" - Load it. - - ---- A note on trajectory format: ----- -If the trajectory is a DUMP file, then make sure the it contains the -information you need for pbctools (see below. I've been using this -command in my LAMMPS scripts to create the trajectories: - - dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz - -It's a good idea to use an atom_style which supports molecule-ID numbers -so that you can assign a molecule-ID number to each atom. (I think this -is needed to wrap atom coordinates without breaking molecules in half.) - -Of course, you don't have to save your trajectories in DUMP format, -(other formats like DCD work fine) I just mention dump files -because these are the files I'm familiar with. - -3) ----- Wrap the coordinates to the unit cell - (without cutting the molecules in half) - -a) Start VMD -b) Load the trajectory in VMD (see above) -c) Menu Extensions->Tk Console -d) Try entering these commands: - - pbc wrap -compound res -all - pbc box - - ----- Optional ---- - Sometimes the solvent or membrane obscures the view of the solute. - It can help to shift the location of the periodic boundary box - To shift the box in the y direction (for example) do this: - - pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0} - pbc box -shiftcenterrel {0.0 0.15 0.0} - - Distances are measured in units of box-length fractions, not Angstroms. - - Alternately if you have a solute whose atoms are all of type 1, - then you can also try this to center the box around it: - - pbc wrap -sel type=1 -all -centersel type=2 -center com - -4) - You should check if your periodic boundary conditions are too small. - To do that: - select Graphics->Representations menu option - click on the "Periodic" tab, and - click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes. - -5) Optional: If you like, change the atom types in the PSF file so - that VMD recognizes the atom types, use something like: - -sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf -sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf -sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf - -(If you do this, it might effect step 2 above.) diff --git a/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg deleted file mode 100644 index bf07914dac..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/AlCell_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg deleted file mode 100644 index 11174969a3..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/lvl1_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg deleted file mode 100644 index 744c9af633..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/lvl2_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg deleted file mode 100644 index a72a1ea8d0..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/lvl3_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg deleted file mode 100644 index 9020a3be0e..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=0_zoom1_LR2.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg b/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg deleted file mode 100644 index 0036c903a2..0000000000 Binary files a/tools/moltemplate/examples/silly/sierpinski/images/serpinski_cube_lattice_8cells_t=7400_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt deleted file mode 100644 index 3054a45e01..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/al_cell.lt +++ /dev/null @@ -1,64 +0,0 @@ -# "AlCell" defines the 4-atom FCC unit cell -# of Aluminum (with a 4.05 angstrom spacing) - -AlCell { - - # AtomID MolID(IGNORE!) AtomType Charge X Y Z - - write("Data Atoms") { - $atom:AlC $mol:... @atom:Al 0.0 0.000 0.000 0.000 - $atom:AlX $mol:... @atom:Al 0.0 0.000 2.025 2.025 - $atom:AlY $mol:... @atom:Al 0.0 2.025 0.000 2.025 - $atom:AlZ $mol:... @atom:Al 0.0 2.025 2.025 0.000 - } - - write_once("In Init") { - units metal - atom_style full # <- Requires each atom has a MolID and Charge. - # This is not necessary. (Why use "full"? - # The "full" atom style is useful if you want to - # mix the aluminum with other molecules later. - # Otherwise, just use "atom_style atomic", and - # and remove the 2nd and 4th columns above.) - pair_style eam/alloy - } - - write_once("In Settings") { - pair_coeff * * Al99.eam.alloy Al - } - - write_once("Data Masses") { - @atom:Al 27.0 - } - -} # AlCell - - - - - -# Here is an alternate way to define AlCell -# using "scale(4.05)" to select the lattice spacing: -# -#FccCell { -# write("Data Atoms") { -# $atom:AlC $mol:... @atom:Al 0.0 0.0 0.0 0.0 -# $atom:AlX $mol:... @atom:Al 0.0 0.0 0.5 0.5 -# $atom:AlY $mol:... @atom:Al 0.0 0.5 0.0 0.5 -# $atom:AyZ $mol:... @atom:Al 0.0 0.5 0.5 0.0 -# } -# write_once("Data Masses") { -# @atom:Al 27.0 -# } -# write_once("In Init") { -# units metal -# atom_style full -# pair_style eam/alloy -# } -# write_once("In Settings") { -# pair_coeff * * Al99.eam.alloy Al -# } -#} -# -#AlCell = FccCell.scale(4.05) -# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt deleted file mode 100644 index 28c2d5ea24..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/sierpinski_cubes.lt +++ /dev/null @@ -1,34 +0,0 @@ -import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell - -# This approach uses the "delete" command. -# It works and it is elegant, but because the majority of atoms will be -# deleted, (and because memory is allocated for all atoms, including -# deleted atoms) this approach is not very memory efficient. - -SierpinskiCubeLvl1 { - cells = new AlCell [3].move(0.00, 0.00, 4.05) - [3].move(0.00, 4.05, 0.00) - [3].move(4.05, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - -SierpinskiCubeLvl2 { - cells = new SierpinskiCubeLvl1 [3].move(0.00, 0.00, 12.15) - [3].move(0.00, 12.15, 0.00) - [3].move(12.15, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - -SierpinskiCubeLvl3 { - cells = new SierpinskiCubeLvl2 [3].move(0.00, 0.00, 36.45) - [3].move(0.00, 36.45, 0.00) - [3].move(36.45, 0.00, 0.00) - delete cells[*][1][1] - delete cells[1][*][1] - delete cells[1][1][*] -} - diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt deleted file mode 100644 index b14929e986..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/elegant_inefficient_version/system.lt +++ /dev/null @@ -1,34 +0,0 @@ -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 72.9 xlo xhi - 0.0 72.9 ylo yhi - 0.0 72.9 zlo zhi -} - -import "sierpinski_cubes.lt" - -cells = new SierpinskiCubeLvl2 [2].move(0.00, 0.00, 36.45) - [2].move(0.00, 36.45, 0.00) - [2].move(36.45, 0.00, 0.00) -delete cells[*][1][1] -delete cells[1][*][1] -delete cells[1][1][*] - - - - - - - - - - - - -################################################################ -# The next command is not necessary: -# - create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # Molecule ID numbers are not necessary. Ignore this. -# diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt deleted file mode 100644 index d45a8331b1..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/sierpinski_cubes.lt +++ /dev/null @@ -1,66 +0,0 @@ -import "al_cell.lt" # <- defines the 4-atom "AlCell" FCC Aluminum unit cell - -# A Sierpinski cube resembles a 3x3x3 Rubik's-cube-like object with the smaller -# cube in each central face (and in the interior) removed. There are 3x3x3-7=20 -# remaining sub-cubes. Each of these 20 sub-cubes is a smaller SierpinskiCube. -# To build a SierpinskiCube, you can list all 20 sub-cubes, or you can fill a -# 3x3x3 cube with sub-cubes and delete the interior sub-cubes. (The later -# approach is used in file "elegant_inefficient_version/sierpinski_cubes.lt") - - - -SierpinskiCubeLvl1 { - # Again, a Sierpinski-cube is constructed of 20 smaller cube-shaped objects. - # Here, the small cube-shaped objects are "AlCells" (defined in "al_cell.lt"). - # I could list out the positions of all 20 AlCells, (and this would be clearer - # for the reader). However instead I built it from a combination of - # two-dimensional and three-dimensional arrays of AlCells (explained below). - - # The next command creates 4 AlCells at: (0, 4.05, 0.0), (8.1, 4.05, 0.0), - # (0, 4.05, 8.1), (8.1, 4.05, 8.1) - - cells_xz = new AlCell.move(0.00, 4.05, 0.00) [2].move(8.10, 0.0, 0.0 ) - [2].move(0.0, 0.0, 8.10) - - # The next command creates 4 AlCells at: (4.05, 0, 0.0), (4.05, 8.1, 0.0), - # (4.05, 0, 8.1), (4.05, 8.1, 8.1) - - cells_yz = new AlCell.move(4.05, 0.00, 0.00) [2].move(0.0, 8.10, 0.0 ) - [2].move(0.0, 0.0, 8.10) - - # The next command creates 12 AlCells (2x2x3) at: - # (0.0, 0.0, 0.0), (0.0, 0.0, 4.05), (0.0, 0.0, 8.1) - # (0.0, 8.1, 0.0), (0.0, 8.1, 4.05), (0.0, 8.1, 8.1) - # (8.1, 8.1, 0.0), (8.1, 8.1, 4.05), (8.1, 8.1, 8.1) - - cells_z = new AlCell [2].move(8.10, 0.00, 0.00) - [2].move(0.00, 8.10, 0.00) - [3].move(0.00, 0.00, 4.05) -} - - - -SierpinskiCubeLvl2 { - # Identical arrangement to SierpinskiCube1 (with 3x larger length scales) - cells_xz= new SierpinskiCubeLvl1.move(0.0,12.15,0.0) [2].move(24.3, 0.0, 0.0 ) - [2].move(0.0, 0.0, 24.3) - cells_yz= new SierpinskiCubeLvl1.move(12.15,0.0,0.0) [2].move(0.0, 24.3, 0.0 ) - [2].move(0.0, 0.0, 24.3) - cells_z = new SierpinskiCubeLvl1 [2].move(24.3, 0.00, 0.00) - [2].move(0.00, 24.3, 0.00) - [3].move(0.00, 0.00, 12.15) -} - - - -SierpinskiCubeLvl3 { - # Identical arrangement to SierpinskiCube2 (with 3x larger length scales) - cells_xz= new SierpinskiCubeLvl2.move(0.0,36.45,0.0) [2].move(72.9, 0.0, 0.0 ) - [2].move(0.0, 0.0, 72.9) - cells_yz= new SierpinskiCubeLvl2.move(36.45,0.0,0.0) [2].move(0.0, 72.9, 0.0 ) - [2].move(0.0, 0.0, 72.9) - cells_z = new SierpinskiCubeLvl2 [2].move(72.9, 0.00, 0.00) - [2].move(0.00, 72.9, 0.00) - [3].move(0.00, 0.00, 36.45) -} - diff --git a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt b/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt deleted file mode 100644 index b226b77eed..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/moltemplate_files/system.lt +++ /dev/null @@ -1,36 +0,0 @@ -# Periodic boundary conditions: -write_once("Data Boundary") { - 0.0 218.7 xlo xhi - 0.0 218.7 ylo yhi - 0.0 218.7 zlo zhi -} - -import "sierpinski_cubes.lt" - -cells_xyz = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 0.0000) -cells_Xyz = new SierpinskiCubeLvl3.move(109.35, 0.0000, 0.0000) -cells_xYz = new SierpinskiCubeLvl3.move(0.0000, 109.35, 0.0000) -cells_xyZ = new SierpinskiCubeLvl3.move(0.0000, 0.0000, 109.35) - - - - - - - - - - - - - - - - -################################################################ -# The next command is not necessary: -# - create_var { $mol } # <-This forces all of the Al atoms in the crystal -# # to share the same molecule ID number. -# # Molecule ID numbers are not necessary. Ignore this. -# diff --git a/tools/moltemplate/examples/silly/sierpinski/run.in b/tools/moltemplate/examples/silly/sierpinski/run.in deleted file mode 100644 index 6b9ad17e6e..0000000000 --- a/tools/moltemplate/examples/silly/sierpinski/run.in +++ /dev/null @@ -1,38 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- -# -# Some of the run-settings below were stolen from: -# -# http://icme.hpc.msstate.edu/mediawiki/index.php/Uniaxial_Compression - -# EQUILIBRATION -reset_timestep 0 -timestep 0.001 -velocity all create 300 12345 mom yes rot no -fix 1 all npt temp 300 300 1 iso 0 0 1 drag 1 - -# Output files -thermo 100 -thermo_style custom step ke pe press -dump dCoords all custom 100 traj.lammpstrj id type x y z ix iy iz - -run 20000 - -# Run for at least 10 picosecond (assuming 1 fs timestep) -run 10000 - - -###################################### -# SIMULATION DONE -print "All done" diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py deleted file mode 100755 index 4fe3ec743d..0000000000 --- a/tools/moltemplate/src/extract_lammps_data.py +++ /dev/null @@ -1,119 +0,0 @@ -#!/usr/bin/env python - -lammps_data_sections = set(['Atoms', - 'Masses', - 'Bonds', - 'Bond Coeffs', - 'Angles', - 'Angle Coeffs', - 'Dihedrals', - 'Dihedral Coeffs', - 'Impropers', - 'Improper Coeffs', - 'BondBond Coeffs', # class2 angles - 'BondAngle Coeffs', # class2 angles - 'MiddleBondTorsion Coeffs', # class2 dihedrals - 'EndBondTorsion Coeffs', # class2 dihedrals - 'AngleTorsion Coeffs', # class2 dihedrals - 'AngleAngleTorsion Coeffs', # class2 dihedrals - 'BondBond13 Coeffs', # class2 dihedrals - 'AngleAngle Coeffs', # class2 impropers - 'Angles By Type', # new. not standard LAMMPS - 'Dihedrals By Type',# new. not standard LAMMPS - 'Angles By Type']) # new. not standard LAMMPS - - -def DeleteComments(string, - escape='\\', - comment_char='#'): - escaped_state = False - for i in range(0,len(string)): - if string[i] in escape: - if escaped_state: - escaped_state = False - else: - escaped_state = True - elif string[i] == comment_char: - if not escaped_state: - return string[0:i] - return string - - - -def ExtractDataSection(f, - section_name, - comment_char = '#', - include_section_name = False, - return_line_nums = False): - - inside_section = False - if section_name in ('header','Header'): #"Header" section includes beginning - inside_section = True - - nonblank_encountered = False - nonheader_encountered = False - - i = 0 - for line_orig in f: - return_this_line = False - line = DeleteComments(line_orig).strip() - if line in lammps_data_sections: - nonheader_encountered = True - if section_name in ('header', 'Header'): - # The "header" section includes all lines at the beginning of the - # before any other section is encountered. - if nonheader_encountered: - return_this_line = False - else: - return_this_line = True - elif line == section_name: - inside_section = True - nonblank_encountered = False - if include_section_name: - return_this_line = True - # A block of blank lines (which dont immediately follow - # the section_name) signal the end of a section: - elif len(line) == 0: - if inside_section and include_section_name: - return_this_line = True - if nonblank_encountered: - inside_section = False - elif line[0] != comment_char: - if inside_section: - nonblank_encountered = True - return_this_line = True - - if return_this_line: - if return_line_nums: - yield i - else: - yield line_orig - - i += 1 - - - -if __name__ == "__main__": - - import sys - lines = sys.stdin.readlines() - exclude_sections = False - if sys.argv[1] == '-n': - exclude_sections = True - del sys.argv[1] - - if not exclude_sections: - for section_name in sys.argv[1:]: - for line in ExtractDataSection(lines, section_name): - sys.stdout.write(line) - else: - line_nums_exclude = set([]) - for section_name in sys.argv[1:]: - for line_num in ExtractDataSection(lines, - section_name, - include_section_name=True, - return_line_nums=True): - line_nums_exclude.add(line_num) - for i in range(0, len(lines)): - if i not in line_nums_exclude: - sys.stdout.write(lines[i]) diff --git a/tools/moltemplate/src/ltemplify.py b/tools/moltemplate/src/ltemplify.py deleted file mode 100755 index 000d0692a7..0000000000 --- a/tools/moltemplate/src/ltemplify.py +++ /dev/null @@ -1,2034 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -# Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2012, Regents of the University of California -# All rights reserved. - -""" -ltemplify.py - -The "ltemplify.py" script can be used to convert existing LAMMPS -input script and data files into a single .ttree file -(which includes both topology and force-field information - for a single molecule in your system). - -Example: - - ltemplify.py -name Mol file.in file.data > mol.ttree - -This creates a template for a new type of molecule (named "Mol"), -consisting of all the atoms in the lammps files you included, -and saves this data in a single ttree file ("mol.ttree"). -This file can be used with moltemplate/ttree to -define large systems containing this molecule. - -""" - -import sys -from ttree_lex import * -from lttree_styles import * - - - -def Intify(s): - if s.isdigit(): - return int(s) - elif s[0:2] == 'id': - return int(s[2:]) - elif s[0:4] == 'type': - return int(s[4:]) - else: - return s - -def StringToInterval(sel_str, slice_delim='*'): - i_slice = sel_str.find(slice_delim) - - if i_slice == -1: - if sel_str.isdigit(): - a = int(sel_str) - b = int(sel_str) - else: - a = sel_str - b = sel_str - - else: - a = sel_str[:i_slice] - b = sel_str[i_slice+len(slice_delim):] - - if (((len(a)>0) and (not a.isdigit())) or - ((len(b)>0) and (not b.isdigit()))): - raise InputError('Error: invalid selection string \"'+ - sel_str+'\"\n') - if (len(a) > 0): - a = int(a) - else: - a = None - - if (len(b) > 0): - b = int(b) - else: - b = None - - return a,b - - -# Selections are simply lists of 2-tuples (pairs) - -def LammpsSelectToIntervals(sel_str, slice_delim='*', or_delim=', '): - - """ - This function converts a string such as "1*4 6 9*12" into - a list of tuples, for example: [(1,4), (6,6), (9,12)] - In general, the of intervals has the form: - [(a1,b1), (a2,b2), (a3,b3), ... ] - - An atom is considered to belong to this selection - if it happens to lie within the closed interval [a,b] - for any pair of a,b values in the list of intervals. - If for a given pair a,b, either a or b is "None", then that a or b - value is not used to disqualify membership in the interval. - (Similar to -infinity or +infinity. In other words if a is set to None, - then to belong to the interval it is enough to be less than b.) - - """ - selection_list = [] - #tokens = sel_str.split(or_delim) <-- Not what we want when len(or_delim)>1 - tokens = LineLex.TextBlock2Lines(sel_str, or_delim, keep_delim=False) - for token in tokens: - token = token.strip() - (a,b) = StringToInterval(token, slice_delim) - selection_list.append((a, b)) - - return selection_list - - -def IntervalListToMinMax(interval_list): - min_a = None - max_b = None - for (a,b) in interval_list: - if ((not (type(a) is int)) or (not (type(b) is int))): - return None,None #only integer min/max makes sense. otherwise skip - - if (min_a == None) or (a < min_a): - min_a = a - if (max_b == None) or (b > max_b): - max_b = b - return min_a, max_b - - -def BelongsToSel(i, sel): - if (i == None) or (sel == None) or (len(sel) == 0): - # If the user has not specified a selection for this category, - # then by default all objects are accepted - return True - - elif (type(i) is str): - if i.isdigit(): - i = int(i) - else: - return True - - belongs = False - for interval in sel: - assert(len(interval) == 2) - if interval[0]: - if i >= interval[0]: - if (interval[1] == None) or (i <= interval[1]): - belongs = True - break - elif interval[1]: - if i <= interval[1]: - belongs = True - break - else: - # In that case, the user entered something like "*" - # which covers all possible numbers - belongs = True - break - - return belongs - - - -try: - - g_program_name = __file__.split('/')[-1] # = 'lemplify.py' - g_version_str = '0.3' - g_date_str = '2012-12-11' - sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') - - non_empty_output = False - no_warnings = True - indent = 2 - cindent = 0 - atomid_selection = [] - atomtype_selection = [] - molid_selection = [] - mol_name = '' - - min_sel_atomid = None - min_sel_atomtype = None - min_sel_bondid = None - min_sel_bondtype = None - min_sel_angleid = None - min_sel_angletype = None - min_sel_dihedralid = None - min_sel_dihedraltype = None - min_sel_improperid = None - min_sel_impropertype = None - - max_sel_atomid = None - max_sel_atomtype = None - max_sel_bondid = None - max_sel_bondtype = None - max_sel_angleid = None - max_sel_angletype = None - max_sel_dihedralid = None - max_sel_dihedraltype = None - max_sel_improperid = None - max_sel_impropertype = None - - needed_atomids = set([]) - needed_atomtypes = set([]) - needed_bondids = set([]) - needed_bondtypes = set([]) - needed_angleids = set([]) - needed_angletypes = set([]) - needed_dihedralids = set([]) - needed_dihedraltypes = set([]) - needed_improperids = set([]) - needed_impropertypes = set([]) - - min_needed_atomtype = None - max_needed_atomtype = None - min_needed_bondtype = None - max_needed_bondtype = None - min_needed_angletype = None - max_needed_angletype = None - min_needed_dihedraltype = None - max_needed_dihedraltype = None - - - # To process the selections, we need to know the atom style: - atom_style_undefined = True - - i_atomid = None - i_atomtype = None - i_molid = None - - l_in_init = [] - l_in_settings = [] - l_in_masses = [] - l_in_pair_coeffs = [] - l_in_bond_coeffs = [] - l_in_angle_coeffs = [] - l_in_dihedral_coeffs = [] - l_in_improper_coeffs = [] - l_data_masses = [] - l_data_bond_coeffs = [] - l_data_angle_coeffs = [] - l_data_dihedral_coeffs = [] - l_data_improper_coeffs = [] - l_data_pair_coeffs = [] - l_data_atoms = [] - l_data_velocities = [] - l_data_bonds = [] - l_data_angles = [] - l_data_dihedrals = [] - l_data_impropers = [] - - # class2 force fields - l_data_bondbond_coeffs = [] - l_data_bondangle_coeffs = [] - l_data_middlebondtorsion_coeffs = [] - l_data_endbondtorsion_coeffs = [] - l_data_angletorsion_coeffs = [] - l_data_angleangletorsion_coeffs = [] - l_data_bondbond13_coeffs = [] - l_data_angleangle_coeffs = [] - - # non-point-like particles: - l_data_ellipsoids = [] - l_data_lines = [] - l_data_triangles = [] - - # automatic generation of bonded interactions by type: - l_data_angles_by_type = [] - l_data_dihedrals_by_type = [] - l_data_impropers_by_type = [] - - atoms_already_read = False - some_pair_coeffs_read = False - complained_atom_style_mismatch = False - - - argv = sys.argv - - i = 1 - - while i < len(argv): - - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - - if argv[i] == '-columns': - if i+1 >= len(argv): - raise InputError('Error: the \"'+argv[i]+'\" argument should be followed by a quoted\n' - ' string which contains a space-delimited list of the names of\n' - ' of columns in the \"Atoms\" section of the LAMMPS data file.\n' - ' If the list contains the symbols:\n' - ' \"atom-ID\" or \"atomid\", they are interpreted\n' - ' as unique atom ID numbers, and columns named\n' - ' \"atom-type\" or \"atomtype\" are interpreted\n' - ' as atom types. Finally, columns named\n' - ' \"molecule-ID\", \"molecule\", or \"mol-ID\", or \"mol\"\n' - ' are interpreted as unique molecule id numbers.\n' - 'Example:\n' - ' '+argv[i]+' \'atom-ID atom-type q polarizability molecule-ID x y z\'\n' - ' defines a custom atom_style containing the properties\n' - ' atom-ID atom-type q polarizability molecule-ID x y z\n' - ' Make sure you enclose the entire list in quotes.\n'); - column_names = argv[i+1].strip('\"\'').strip().split() - del(argv[i:i+2]) - - elif ((argv[i] == '-name') or - (argv[i] == '-molname') or - (argv[i] == '-molecule-name') or - (argv[i] == '-molecule_name')): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by a a molecule type name.\n') - cindent = 2 - indent += cindent - mol_name = argv[i+1] - del(argv[i:i+2]) - - elif ((argv[i].lower() == '-atomstyle') or - (argv[i].lower() == '-atom_style') or - (argv[i].lower() == '-atom-style')): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n' - ' (or single quoted string which includes a space-separated\n' - ' list of column names).\n') - atom_style_undefined = False - column_names = AtomStyle2ColNames(argv[i+1]) - if (argv[i+1].strip().split()[0] in g_style_map): - l_in_init.append((' '*indent) + 'atom_style ' + argv[i+1] + '\n') - sys.stderr.write('\n \"Atoms\" column format:\n') - sys.stderr.write(' '+(' '.join(column_names))+'\n') - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - if i_molid: - sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') - else: - sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n') - del(argv[i:i+2]) - - elif ((argv[i].lower() == '-id') or - #(argv[i].lower() == '-a') or - #(argv[i].lower() == '-atoms') or - (argv[i].lower() == '-atomid') or - #(argv[i].lower() == '-atomids') or - (argv[i].lower() == '-atom-id') - #(argv[i].lower() == '-atom-ids') or - #(argv[i].lower() == '-$atom') or - #(argv[i].lower() == '-$atoms') - ): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers\n' - ' (or strings). These identify the group of atoms you want to\n' - ' to include in the template you are creating.\n') - atomid_selection += LammpsSelectToIntervals(argv[i+1]) - min_sel_atomid, max_sel_atomid = IntervalListToMinMax(atomid_selection) - del(argv[i:i+2]) - elif ((argv[i].lower() == '-type') or - #(argv[i].lower() == '-t') or - (argv[i].lower() == '-atomtype') or - (argv[i].lower() == '-atom-type') - #(argv[i].lower() == '-atomtypes') or - #(argv[i].lower() == '-atom-types') or - #(argv[i].lower() == '-@atom') or - #(argv[i].lower() == '-@atoms') or - #(argv[i].lower() == '-@atomtype') or - #(argv[i].lower() == '-@atomtypes') - ): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by a list of integers.\n' - ' (or strings). These identify the group of atom types you want to\n' - ' to include in the template you are creating.\n') - atomtype_selection += LammpsSelectToIntervals(argv[i+1]) - min_sel_atomtype, max_sel_atomtype = IntervalListToMinMax(atomtype_selection) - del(argv[i:i+2]) - elif ((argv[i].lower() == '-mol') or - #(argv[i].lower() == '-m') or - (argv[i].lower() == '-molid') or - #(argv[i].lower() == '-molids') or - (argv[i].lower() == '-mol-id') or - #(argv[i].lower() == '-mol-ids') or - #(argv[i].lower() == '-molecule') or - (argv[i].lower() == '-moleculeid') or - (argv[i].lower() == '-molecule-id') - #(argv[i].lower() == '-molecules') or - #(argv[i].lower() == '-molecule-ids') or - #(argv[i].lower() == '-$mol') or - #(argv[i].lower() == '-$molecule') - ): - if i+1 >= len(argv): - sys.stderr.write('Error: '+argv[i]+' flag should be followed by a list of integers.\n' - ' (or strings). These identify the group of molecules you want to\n' - ' include in the template you are creating.\n') - molid_selection += LammpsSelectToIntervals(argv[i+1]) - del(argv[i:i+2]) - else: - i += 1 - - if atom_style_undefined: - # The default atom_style is "full" - column_names = AtomStyle2ColNames('full') - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - - #--------------------------------------------------------- - #-- The remaining arguments are files that the user wants - #-- us to read and convert. It is typical to have - #-- multiple input files, because LAMMPS users often - #-- store their force field parameters in either the LAMMPS - #-- data files and input script files, or both. - #-- We want to search all of the LAMMPS input files in - #-- order to make sure we extracted all the force field - #-- parameters (coeff commands). - #--------------------------------------------------------- - - for i_arg in range(1,len(argv)): - fname = argv[i_arg] - try: - lammps_file = open(fname, 'r') - except IOError: - raise InputError('Error: unrecognized argument (\"'+fname+'\"),\n' - ' OR unable to open file:\n' - '\n' - ' \"'+fname+'\"\n' - ' for reading.\n' - '\n' - ' (If you were not trying to open a file with this name,\n' - ' then there is a problem in your argument list.)\n') - - sys.stderr.write('reading file \"'+fname+'\"\n') - - atomid2type = {} - atomid2mol = {} - data_file_header_names = set(['LAMMPS Description', - 'Atoms', 'Masses', 'Velocities', 'Bonds', - 'Angles', 'Dihedrals', 'Impropers', - 'Pair Coeffs', - 'Bond Coeffs', 'Angle Coeffs', - 'Dihedral Coeffs', 'Improper Coeffs', - #class2 force fields: - 'BondBond Coeffs', 'BondAngle Coeffs', - 'MiddleBondTorsion Coeffs', 'EndBondTorsion Coeffs', - 'AngleTorsion Coeffs', 'AngleAngleTorsion Coeffs', - 'BondBond13 Coeffs', - 'AngleAngle Coeffs', - # non-point-like particles: - 'Ellipsoids', 'Triangles', 'Lines', - #specifying bonded interactions by type: - 'Angles By Type', 'Dihedrals By Type', 'Impropers By Type' - ]) - - lex=LineLex(lammps_file, fname) - lex.source_triggers = set(['include','import']) - # set up lex to accept most characters in file names: - lex.wordterminators = '(){}' + lex.whitespace - # set up lex to understand the "include" statement: - lex.source = 'include' - lex.escape = '\\' - - while lex: - infile = lex.infile - lineno = lex.lineno - line = lex.ReadLine() - if (lex.infile != infile): - infile = lex.infile - lineno = lex.lineno - - #sys.stderr.write(' processing \"'+line.strip()+'\", (\"'+infile+'\":'+str(lineno)+')\n') - - if line == '': - break - - tokens = line.strip().split() - if (len(tokens) > 0): - if ((tokens[0] == 'atom_style') and - atom_style_undefined): - - sys.stderr.write(' Atom Style found. Processing: \"'+line.strip()+'\"\n') - if atoms_already_read: - raise InputError('Error: The file containing the \"atom_style\" command must\n' - ' come before the data file in the argument list.\n' - ' (The templify program needs to know the atom style before reading\n' - ' the data file. Either change the order of arguments so that the\n' - ' LAMMPS input script file is processed before the data file, or use\n' - ' the \"-atom_style\" command line argument to specify the atom_style.)\n') - - column_names = AtomStyle2ColNames(line.split()[1]) - i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names) - - sys.stderr.write('\n \"Atoms\" column format:\n') - sys.stderr.write(' '+(' '.join(column_names))+'\n') - if i_molid: - sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+', i_molid='+str(i_molid+1)+')\n\n') - else: - sys.stderr.write(' (i_atomid='+str(i_atomid+1)+', i_atomtype='+str(i_atomtype+1)+')\n\n') - l_in_init.append((' '*indent)+line.lstrip()) - - elif (tokens[0] in set(['units', - 'angle_style', - 'bond_style', - 'dihedral_style', - 'impoper_style', - 'min_style', - 'pair_style', - 'pair_modify', - 'special_bonds', - 'kspace_style', - 'kspace_modify'])): - l_in_init.append((' '*indent)+line.lstrip()) - - #if (line.strip() == 'LAMMPS Description'): - # sys.stderr.write(' processing \"'+line.strip()+'\"\n') - # # skip over this section - # while lex: - # line = lex.ReadLine() - # if line.strip() in data_file_header_names: - # lex.push_raw_text(line) # <- Save line for later - # break - - elif (line.strip() == 'Atoms'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - atoms_already_read = True - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if ((len(tokens) <= i_atomid) or - (len(tokens) <= i_atomtype) or - ((i_molid != None) and - (len(tokens) <= i_molid))): - raise InputError('Error: The number of columns in the \"Atoms\" section does\n' - ' not match the atom_style (see column name list above).\n') - elif ((len(tokens) != len(column_names)) and - (not complained_atom_style_mismatch)): - complained_atom_style_mismatch = True - sys.stderr.write('Warning: The number of columns in the \"Atoms\" section does\n' - ' not match the atom_style (see column name list above).\n') - # this is not a very serious warning. - #no_warnings = False <--no need. commenting out - - - atomid = Intify(tokens[i_atomid]) - atomtype = Intify(tokens[i_atomtype]) - - molid = None - if i_molid: - molid = Intify(tokens[i_molid]) - - atomid2type[atomid] = atomtype - if i_molid: - atomid2mol[atomid] = molid - - - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[i_atomid] = '$atom:id'+tokens[i_atomid] - tokens[i_atomtype] = '@atom:type'+tokens[i_atomtype] - if i_molid: - tokens[i_molid] = '$mol:id'+tokens[i_molid] - l_data_atoms.append((' '*indent)+(' '.join(tokens)+'\n')) - needed_atomids.add(atomid) - needed_atomtypes.add(int(atomtype)) - - for atomtype in needed_atomtypes: - if type(atomtype) is int: - if ((min_needed_atomtype == None) or - (min_needed_atomtype > atomtype)): - min_needed_atomtype = atomtype - if ((max_needed_atomtype == None) or - (max_needed_atomtype < atomtype)): - max_needed_atomtype = atomtype - - - elif (line.strip() == 'Masses'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomtype = Intify(tokens[0]) - if BelongsToSel(atomtype, atomtype_selection): - #tokens[0] = '@atom:type'+tokens[0] - l_data_masses.append((' '*indent)+(' '.join(tokens)+'\n')) - elif (line.strip() == 'Velocities'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id'+tokens[0] - l_data_velocities.append((' '*indent)+(' '.join(tokens)+'\n')) - - # non-point-like-particles: - elif (line.strip() == 'Ellipsoids'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id'+tokens[0] - l_data_ellipsoids.append((' '*indent)+(' '.join(tokens)+'\n')) - elif (line.strip() == 'Lines'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id'+tokens[0] - l_data_lines.append((' '*indent)+(' '.join(tokens)+'\n')) - elif (line.strip() == 'Triangles'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - atomid = Intify(tokens[0]) - atomtype = None - if atomid in atomid2type: - atomtype = atomid2type[atomid] - moldid = None - if atomid in atomid2mol: - molid = atomid2mol[atomid] - if (BelongsToSel(atomid, atomid_selection) and - BelongsToSel(atomtype, atomtype_selection) and - BelongsToSel(molid, molid_selection)): - tokens[0] = '$atom:id'+tokens[0] - l_data_triangles.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Bonds'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 4): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Bonds section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$bond:id'+tokens[0] - #tokens[1] = '@bond:type'+tokens[1] - atomids = [None, None] - atomtypes = [None, None] - molids = [None, None] - in_selections = True - some_in_selection = False - for n in range(0,2): - atomids[n] = Intify(tokens[2+n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n') - sys.stderr.write(' (between atom ids: ') - - for n in range(0,2): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected are bonded\n' - ' to other atoms you didn\'t select.\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - - - elif (line.strip() == 'Angles'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line == '': - break - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 5): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Angles section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$angle:id'+tokens[0] - #tokens[1] = '@angle:type'+tokens[1] - atomids = [None, None, None] - atomtypes = [None, None, None] - molids = [None, None, None] - in_selections = True - some_in_selection = False - for n in range(0,3): - atomids[n] = Intify(tokens[2+n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,3): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 3-body \"Angle\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - - elif (line.strip() == 'Dihedrals'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Dihedrals section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$dihedral:id'+tokens[0] - #tokens[1] = '@dihedral:type'+tokens[1] - atomids = [None, None, None, None] - atomtypes = [None, None, None, None] - molids = [None, None, None, None] - in_selections = True - some_in_selection = False - for n in range(0,4): - atomids[n] = Intify(tokens[2+n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,4): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 4-body \"Dihedral\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - - elif (line.strip() == 'Impropers'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Impropers section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$improper:id'+tokens[0] - #tokens[1] = '@improper:type'+tokens[1] - atomids = [None, None, None, None] - atomtypes = [None, None, None, None] - molids = [None, None, None, None] - in_selections = True - some_in_selection = False - for n in range(0,4): - atomids[n] = Intify(tokens[2+n]) - if atomids[n] in atomid2type: - atomtypes[n] = atomid2type[atomids[n]] - if atomids[n] in atomid2mol: - molids[n] = atomid2mol[atomids[n]] - if (BelongsToSel(atomids[n], atomid_selection) and - BelongsToSel(atomtypes[n], atomtype_selection) and - BelongsToSel(molids[n], molid_selection)): - #tokens[2+n] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_impropers.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS IMPROPERS\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,4): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 4-body \"Improper\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - no_warnings = False - - - elif (line.strip() == 'Bond Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@bond:type'+tokens[0] - l_data_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Angle Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@angle:type'+tokens[0] - l_data_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Dihedral Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@dihedral:type'+tokens[0] - l_data_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Improper Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - #tokens[0] = '@improper:type'+tokens[0] - l_data_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Pair Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - some_pair_coeffs_read = True - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 2): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Pair Coeffs section:\n' - ' \"'+line.strip()+'\"\n') - atomtype_i_str = tokens[0] - if '*' in atomtype_i_str: - raise InputError('PROBLEM near or before '+ErrorLeader(infile, lineno)+'\n' - ' As of 2012-7, moltemplate forbids use of the "\*\" wildcard\n' - ' character in the \"Pair Coeffs\" section.\n') - else: - i = int(atomtype_i_str) - if ((not i) or - BelongsToSel(i, atomtype_selection)): - i_str = '@atom:type'+str(i) - tokens[0] = i_str - l_data_pair_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (tokens[0] == 'pair_coeff'): - some_pair_coeffs_read = True - if (len(tokens) < 3): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical pair_coeff command:\n' - ' \"'+line.strip()+'\"\n') - l_in_pair_coeffs.append(' '*indent+line.strip()) - - elif (tokens[0] == 'mass'): - some_pair_coeffs_read = True - if (len(tokens) < 3): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical \"mass\" command:\n' - ' \"'+line.strip()+'\"\n') - l_in_masses.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (tokens[0] == 'bond_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical bond_coeff command:\n' - ' \"'+line.strip()+'\"\n') - #tokens[1] = '@bond:type'+tokens[1] - l_in_bond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (tokens[0] == 'angle_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical angle_coeff command:\n' - ' \"'+line.strip()+'\"\n') - #tokens[1] = '@angle:type'+tokens[1] - l_in_angle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (tokens[0] == 'dihedral_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical dihedral_coeff command:\n' - ' \"'+line.strip()+'\"\n') - #tokens[1] = '@dihedral:type'+tokens[1] - l_in_dihedral_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - elif (tokens[0] == 'improper_coeff'): - if (len(tokens) < 2): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical improper_coeff command:\n' - ' \"'+line.strip()+'\"\n') - #tokens[1] = '@improper:type'+tokens[1] - l_in_improper_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - - # -- class2 force fields -- - elif (line.strip() == 'BondBond Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@angle:type'+tokens[0] - l_data_bondbond_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'BondAngle Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@angle:type'+tokens[0] - l_data_bondangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'MiddleBondTorsion Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_middlebondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'EndBondTorsion Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_endbondtorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'AngleTorsion Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_angletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'AngleAngleTorsion Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_angleangletorsion_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'BondBond13 Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_bondbond13_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'AngleAngle Coeffs'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@improper:type'+tokens[0] - l_data_angleangle_coeffs.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Angles By Type'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@angle:type'+tokens[0] - l_data_angles_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Dihedrals By Type'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@dihedral:type'+tokens[0] - l_data_dihedrals_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) - - elif (line.strip() == 'Impropers By Type'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - tokens[0] = '@improper:type'+tokens[0] - l_data_impropers_by_type.append((' '*indent)+(' '.join(tokens)+'\n')) - - else: - sys.stderr.write(' Ignoring line \"'+line.strip()+'\"\n') - - sys.stderr.write('\n\n') - # --- Now delete items that were not selected from the other lists --- - - # --- MASSES --- - - # delete masses for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_data_masses): - line = l_data_masses[i_line] - tokens = line.strip().split() - atomtype = Intify(tokens[0]) - if ((not (atomtype in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype, atomtype_selection)))): - del(l_data_masses[i_line]) - else: - tokens[0] = '@atom:type'+str(atomtype) - l_data_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - - - # --- PAIR COEFFS --- - - # delete data_pair_coeffs for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_data_pair_coeffs): - line = l_data_pair_coeffs[i_line] - tokens = line.strip().split() - assert(len(tokens) > 0) - split_colon = tokens[0].split(':') - assert(len(split_colon) == 2) - atomtype = Intify(split_colon[1]) - if ((not (atomtype in needed_atomtypes)) and - (not ((len(atomtype_selection) > 0) and - BelongsToSel(atomtype, atomtype_selection)))): - del(l_data_pair_coeffs[i_line]) - else: - i_line += 1 - - # delete in_pair_coeffs for atom we don't care about anymore: - i_line = 0 - while i_line < len(l_in_pair_coeffs): - line = l_in_pair_coeffs[i_line] - tokens = line.strip().split() - atomtype_i_str = tokens[1] - atomtype_j_str = tokens[2] - #if (('*' in atomtype_i_str) or - # ('*' in atomtype_j_str)): - # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' - # ' pair_coeff command contains a \"*\" character.\n' - # ' Keep in mind that using moltemplate.sh you can manually change the\n' - # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' - # ' nor to accidentally change the order of atom types in one of these\n' - # ' pair_coeff commands. For example, commands like\n' - # ' pair_coeff 10*4 20*10 0.15 3.6\n' - # ' can be generated by moltemplate.sh, however\n' - # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' - # ' pair_coeff 4*10 10*20 0.15 3.6)\n' - # ' Later on, you may want to check to make sure moltemplate.sh\n' - # ' is not doing this. (Fortunately you never have to worry unless\n' - # ' you are using the -a or -b arguments with moltemplate.sh)\n') - - if ('*' in atomtype_i_str): - atomtype_i_tokens = atomtype_i_str.split('*') - - if atomtype_i_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - i_a = min_sel_atomtype - else: - i_a = min_needed_atomtype - else: - i_a = Intify(atomtype_i_tokens[0]) - - if atomtype_i_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - i_b = max_sel_atomtype - else: - i_b = max_needed_atomtype - else: - i_b = Intify(atomtype_i_tokens[1]) - - else: - i_a = i_b = Intify(atomtype_i_str) - - i_a_final = None - i_b_final = None - for i in range(i_a, i_b+1): - if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): - i_a_final = i - break - for i in reversed(range(i_a, i_b+1)): - if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): - i_b_final = i - break - - #if i_a_final and i_b_final: - # if i_a_final == i_b_final: - # i_str = '@atom:type'+str(i_a_final) - # tokens[1] = i_str - # else: - # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' - - - - if ('*' in atomtype_j_str): - atomtype_j_tokens = atomtype_j_str.split('*') - - if atomtype_j_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - j_a = min_sel_atomtype - else: - j_a = min_needed_atomtype - else: - j_a = Intify(atomtype_j_tokens[0]) - - if atomtype_j_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - j_b = max_sel_atomtype - else: - j_b = max_needed_atomtype - else: - j_b = Intify(atomtype_j_tokens[1]) - - else: - j_a = j_b = Intify(atomtype_j_str) - - j_a_final = None - j_b_final = None - for j in range(j_a, j_b+1): - if ((j in needed_atomtypes) or (min_sel_atomtype <= j)): - j_a_final = j - break - for j in reversed(range(j_a, j_b+1)): - if ((j in needed_atomtypes) or (max_sel_atomtype >= j)): - j_b_final = j - break - - #if j_a_final and j_b_final: - # if j_a_final == j_b_final: - # j_str = '@atom:type'+str(j_a_final) - # tokens[1] = j_str - # else: - # j_str = '@{atom:type'+str(j_a_final)+'}*@{atom:type'+str(j_b_final)+'}' - - - - if not (i_a_final and i_b_final and j_a_final and j_b_final): - del(l_in_pair_coeffs[i_line]) - elif (('*' in atomtype_i_str) or ('*' in atomtype_j_str)): - del(l_in_pair_coeffs[i_line]) - for i in range(i_a_final, i_b_final+1): - for j in range(j_a_final, j_b_final+1): - if j >= i: - tokens[1] = '@atom:type'+str(i) - tokens[2] = '@atom:type'+str(j) - l_in_pair_coeffs.insert(i_line, - (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - tokens[1] = '@atom:type'+tokens[1] - tokens[2] = '@atom:type'+tokens[2] - l_in_pair_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - - - - # delete mass commands for atom types we don't care about anymore: - i_line = 0 - while i_line < len(l_in_masses): - line = l_in_masses[i_line] - tokens = line.strip().split() - atomtype_i_str = tokens[1] - #if (('*' in atomtype_i_str) or - # ('*' in atomtype_j_str)): - # sys.stderr.write('WARNING: near or before '+ErrorLeader(infile, lineno)+'\n' - # ' pair_coeff command contains a \"*\" character.\n' - # ' Keep in mind that using moltemplate.sh you can manually change the\n' - # ' numbers assigned to each atom type (when using -a or -b). Make sure\n' - # ' nor to accidentally change the order of atom types in one of these\n' - # ' pair_coeff commands. For example, commands like\n' - # ' pair_coeff 10*4 20*10 0.15 3.6\n' - # ' can be generated by moltemplate.sh, however\n' - # ' they may be rejected by LAMMPS (because LAMMPS prefers this\n' - # ' pair_coeff 4*10 10*20 0.15 3.6)\n' - # ' Later on, you may want to check to make sure moltemplate.sh\n' - # ' is not doing this. (Fortunately you never have to worry unless\n' - # ' you are using the -a or -b arguments with moltemplate.sh)\n') - - if ('*' in atomtype_i_str): - atomtype_i_tokens = atomtype_i_str.split('*') - - if atomtype_i_tokens[0] == '': - if (min_sel_atomtype and - (min_sel_atomtype < min_needed_atomtype)): - i_a = min_sel_atomtype - else: - i_a = min_needed_atomtype - else: - i_a = Intify(atomtype_i_tokens[0]) - - if atomtype_i_tokens[1] == '': - if (max_sel_atomtype and - (max_sel_atomtype > max_needed_atomtype)): - i_b = max_sel_atomtype - else: - i_b = max_needed_atomtype - else: - i_b = Intify(atomtype_i_tokens[1]) - - else: - i_a = i_b = Intify(atomtype_i_str) - - i_a_final = None - i_b_final = None - for i in range(i_a, i_b+1): - if ((i in needed_atomtypes) or (min_sel_atomtype <= i)): - i_a_final = i - break - for i in reversed(range(i_a, i_b+1)): - if ((i in needed_atomtypes) or (max_sel_atomtype >= i)): - i_b_final = i - break - #if i_a_final and i_b_final: - # if i_a_final == i_b_final: - # i_str = '@atom:type'+str(i_a_final) - # tokens[1] = i_str - # else: - # i_str = '@{atom:type'+str(i_a_final)+'}*@{atom:type'+str(i_b_final)+'}' - - if not (i_a_final and i_b_final and j_a_final and j_b_final): - del(l_in_masses[i_line]) - elif ('*' in atomtype_i_str): - del(l_in_masses[i_line]) - for i in range(i_a_final, i_b_final+1): - tokens[1] = '@atom:type'+str(i) - l_in_masses.insert(i_line, (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - assert(i_a == i_b) - tokens[1] = '@atom:type'+str(i_a) - l_in_masses[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - - - - # --- BONDS AND BOND COEFFS --- - - # delete lines from data_bonds if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_bonds): - line = l_data_bonds[i_line] - tokens = line.strip().split() - assert(len(tokens) == 4) - - bondid = Intify(tokens[0]) - bondtype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - #if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$bond:id'+str(bondid) - tokens[1] = '@bond:type'+str(bondtype) - tokens[2] = '$atom:id'+str(atomid1) - tokens[3] = '$atom:id'+str(atomid2) - needed_bondids.add(bondid) - needed_bondtypes.add(bondtype) - l_data_bonds[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - #else: - # del(l_data_bonds[i_line]) - - # delete data_bond_coeffs for bondtypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_bond_coeffs): - line = l_data_bond_coeffs[i_line] - tokens = line.strip().split() - bondtype = Intify(tokens[0]) - if (not (bondtype in needed_bondtypes)): - del(l_data_bond_coeffs[i_line]) - else: - tokens[0] = '@bond:type'+str(bondtype) - l_data_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - # delete in_bond_coeffs for bondtypes we don't care about anymore: - for bondtype in needed_bondtypes: - if type(bondtype) is int: - if ((min_needed_bondtype == None) or - (min_needed_bondtype > bondtype)): - min_needed_bondtype = bondtype - if ((max_needed_bondtype == None) or - (max_needed_bondtype < bondtype)): - max_needed_bondtype = bondtype - i_line = 0 - while i_line < len(l_in_bond_coeffs): - line = l_in_bond_coeffs[i_line] - tokens = line.strip().split() - bondtype_str = tokens[1] - - if ('*' in bondtype_str): - bondtype_tokens = bondtype_str.split('*') - - if bondtype_tokens[0] == '': - i_a = min_needed_bondtype - else: - i_a = Intify(bondtype_tokens[0]) - - if bondtype_tokens[1] == '': - i_b = max_needed_bondtype - else: - i_b = Intify(bondtype_tokens[1]) - - else: - i_a = i_b = Intify(bondtype_str) - - if i_a < min_needed_bondtype: - i_a = min_needed_bondtype - if i_b > max_needed_bondtype: - i_b = max_needed_bondtype - - #if i_a == i_b: - # i_str = '@bond:type'+str(i_a) - # tokens[1] = i_str - #else: - # i_str = '@{bond:type'+str(j_a)+'}*@{bond:type'+str(j_b)+'}' - - if ('*' in bondtype_str): - del(l_in_bond_coeffs[i_line]) - for i in range(i_a, i_b+1): - if (i in needed_bondtypes): - tokens[1] = '@bond:type'+str(i) - l_in_bond_coeffs.insert(i_line, - (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - assert(i_a == i_b) - if (i_a in needed_bondtypes): - tokens[1] = '@bond:type'+str(i_a) - l_in_bond_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - else: - del(l_in_bond_coeffs[i_line]) - - - - - - # --- ANGLES AND ANGLE COEFFS --- - - # delete lines from data_angles if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_angles): - line = l_data_angles[i_line] - tokens = line.strip().split() - assert(len(tokens) == 5) - - angleid = Intify(tokens[0]) - angletype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - #if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$angle:id'+str(angleid) - tokens[1] = '@angle:type'+str(angletype) - tokens[2] = '$atom:id'+str(atomid1) - tokens[3] = '$atom:id'+str(atomid2) - tokens[4] = '$atom:id'+str(atomid3) - needed_angleids.add(angleid) - needed_angletypes.add(angletype) - l_data_angles[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - #else: - # del(l_data_angles[i_line]) - - # delete data_angle_coeffs for angletypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_angle_coeffs): - line = l_data_angle_coeffs[i_line] - tokens = line.strip().split() - angletype = Intify(tokens[0]) - if (not (angletype in needed_angletypes)): - del(l_data_angle_coeffs[i_line]) - else: - tokens[0] = '@angle:type'+str(angletype) - l_data_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - # delete in_angle_coeffs for angletypes we don't care about anymore: - for angletype in needed_angletypes: - if type(angletype) is int: - if ((min_needed_angletype == None) or - (min_needed_angletype > angletype)): - min_needed_angletype = angletype - if ((max_needed_angletype == None) or - (max_needed_angletype < angletype)): - max_needed_angletype = angletype - i_line = 0 - while i_line < len(l_in_angle_coeffs): - line = l_in_angle_coeffs[i_line] - tokens = line.strip().split() - angletype_str = tokens[1] - - if ('*' in angletype_str): - angletype_tokens = angletype_str.split('*') - - if angletype_tokens[0] == '': - i_a = min_needed_angletype - else: - i_a = Intify(angletype_tokens[0]) - - if angletype_tokens[1] == '': - i_b = max_needed_angletype - else: - i_b = Intify(angletype_tokens[1]) - - else: - i_a = i_b = Intify(angletype_str) - - if i_a < min_needed_angletype: - i_a = min_needed_angletype - if i_b > max_needed_angletype: - i_b = max_needed_angletype - - #if i_a == i_b: - # i_str = '@angle:type'+str(i_a) - # tokens[1] = i_str - #else: - # i_str = '@{angle:type'+str(j_a)+'}*@{angle:type'+str(j_b)+'}' - - if ('*' in angletype_str): - del(l_in_angle_coeffs[i_line]) - for i in range(i_a, i_b+1): - if (i in needed_angletypes): - tokens[1] = '@angle:type'+str(i) - l_in_angle_coeffs.insert(i_line, - (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - assert(i_a == i_b) - if (i_a in needed_angletypes): - tokens[1] = '@angle:type'+str(i_a) - l_in_angle_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - else: - del(l_in_angle_coeffs[i_line]) - - - - # --- DIHEDRALS AND DIHEDRAL COEFFS --- - - # delete lines from data_dihedrals if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_dihedrals): - line = l_data_dihedrals[i_line] - tokens = line.strip().split() - assert(len(tokens) == 6) - - dihedralid = Intify(tokens[0]) - dihedraltype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - atomid4 = Intify(tokens[5]) - #if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$dihedral:id'+str(dihedralid) - tokens[1] = '@dihedral:type'+str(dihedraltype) - tokens[2] = '$atom:id'+str(atomid1) - tokens[3] = '$atom:id'+str(atomid2) - tokens[4] = '$atom:id'+str(atomid3) - tokens[5] = '$atom:id'+str(atomid4) - needed_dihedralids.add(dihedralid) - needed_dihedraltypes.add(dihedraltype) - l_data_dihedrals[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - #else: - # del(l_data_dihedrals[i_line]) - - # delete data_dihedral_coeffs for dihedraltypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_dihedral_coeffs): - line = l_data_dihedral_coeffs[i_line] - tokens = line.strip().split() - dihedraltype = Intify(tokens[0]) - if (not (dihedraltype in needed_dihedraltypes)): - del(l_data_dihedral_coeffs[i_line]) - else: - tokens[0] = '@dihedral:type'+str(dihedraltype) - l_data_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - # delete in_dihedral_coeffs for dihedraltypes we don't care about anymore: - for dihedraltype in needed_dihedraltypes: - if type(dihedraltype) is int: - if ((min_needed_dihedraltype == None) or - (min_needed_dihedraltype > dihedraltype)): - min_needed_dihedraltype = dihedraltype - if ((max_needed_dihedraltype == None) or - (max_needed_dihedraltype < dihedraltype)): - max_needed_dihedraltype = dihedraltype - i_line = 0 - while i_line < len(l_in_dihedral_coeffs): - line = l_in_dihedral_coeffs[i_line] - tokens = line.strip().split() - dihedraltype_str = tokens[1] - - if ('*' in dihedraltype_str): - dihedraltype_tokens = dihedraltype_str.split('*') - - if dihedraltype_tokens[0] == '': - i_a = min_needed_dihedraltype - else: - i_a = Intify(dihedraltype_tokens[0]) - - if dihedraltype_tokens[1] == '': - i_b = max_needed_dihedraltype - else: - i_b = Intify(dihedraltype_tokens[1]) - - else: - i_a = i_b = Intify(dihedraltype_str) - - if i_a < min_needed_dihedraltype: - i_a = min_needed_dihedraltype - if i_b > max_needed_dihedraltype: - i_b = max_needed_dihedraltype - - #if i_a == i_b: - # i_str = '@dihedral:type'+str(i_a) - # tokens[1] = i_str - #else: - # i_str = '@{dihedral:type'+str(j_a)+'}*@{dihedral:type'+str(j_b)+'}' - - if ('*' in dihedraltype_str): - del(l_in_dihedral_coeffs[i_line]) - for i in range(i_a, i_b+1): - if (i in needed_dihedraltypes): - tokens[1] = '@dihedral:type'+str(i) - l_in_dihedral_coeffs.insert(i_line, - (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - assert(i_a == i_b) - if (i_a in needed_dihedraltypes): - tokens[1] = '@dihedral:type'+str(i_a) - l_in_dihedral_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - else: - del(l_in_dihedral_coeffs[i_line]) - - - - # --- IMPROPERS AND IMPROPER COEFFS --- - - # delete lines from data_impropers if they involve atoms we don't care about - i_line = 0 - while i_line < len(l_data_impropers): - line = l_data_impropers[i_line] - tokens = line.strip().split() - assert(len(tokens) == 6) - - improperid = Intify(tokens[0]) - impropertype = Intify(tokens[1]) - atomid1 = Intify(tokens[2]) - atomid2 = Intify(tokens[3]) - atomid3 = Intify(tokens[4]) - atomid4 = Intify(tokens[5]) - #if ((atomid1 in needed_atomids) and - # (atomid2 in needed_atomids)): - tokens[0] = '$improper:id'+str(improperid) - tokens[1] = '@improper:type'+str(impropertype) - tokens[2] = '$atom:id'+str(atomid1) - tokens[3] = '$atom:id'+str(atomid2) - tokens[4] = '$atom:id'+str(atomid3) - tokens[5] = '$atom:id'+str(atomid4) - needed_improperids.add(improperid) - needed_impropertypes.add(impropertype) - l_data_impropers[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - #else: - # del(l_data_impropers[i_line]) - - # delete data_improper_coeffs for impropertypes we don't care about anymore: - i_line = 0 - while i_line < len(l_data_improper_coeffs): - line = l_data_improper_coeffs[i_line] - tokens = line.strip().split() - impropertype = Intify(tokens[0]) - if (not (impropertype in needed_impropertypes)): - del(l_data_improper_coeffs[i_line]) - else: - tokens[0] = '@improper:type'+str(impropertype) - l_data_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - - # delete in_improper_coeffs for impropertypes we don't care about anymore: - for impropertype in needed_impropertypes: - if type(impropertype) is int: - if ((min_needed_impropertype == None) or - (min_needed_impropertype > impropertype)): - min_needed_impropertype = impropertype - if ((max_needed_impropertype == None) or - (max_needed_impropertype < impropertype)): - max_needed_impropertype = impropertype - i_line = 0 - while i_line < len(l_in_improper_coeffs): - line = l_in_improper_coeffs[i_line] - tokens = line.strip().split() - impropertype_str = tokens[1] - - if ('*' in impropertype_str): - impropertype_tokens = impropertype_str.split('*') - - if impropertype_tokens[0] == '': - i_a = min_needed_impropertype - else: - i_a = Intify(impropertype_tokens[0]) - - if impropertype_tokens[1] == '': - i_b = max_needed_impropertype - else: - i_b = Intify(impropertype_tokens[1]) - - else: - i_a = i_b = Intify(impropertype_str) - - if i_a < min_needed_impropertype: - i_a = min_needed_impropertype - if i_b > max_needed_impropertype: - i_b = max_needed_impropertype - - #if i_a == i_b: - # i_str = '@improper:type'+str(i_a) - # tokens[1] = i_str - #else: - # i_str = '@{improper:type'+str(j_a)+'}*@{improper:type'+str(j_b)+'}' - - if ('*' in impropertype_str): - del(l_in_improper_coeffs[i_line]) - for i in range(i_a, i_b+1): - if (i in needed_impropertypes): - tokens[1] = '@improper:type'+str(i) - l_in_improper_coeffs.insert(i_line, - (' '*indent)+(' '.join(tokens)+'\n')) - i_line += 1 - else: - assert(i_a == i_b) - if (i_a in needed_impropertypes): - tokens[1] = '@improper:type'+str(i_a) - l_in_improper_coeffs[i_line] = (' '*indent)+(' '.join(tokens)+'\n') - i_line += 1 - else: - del(l_in_improper_coeffs[i_line]) - - - - - - - - - if not some_pair_coeffs_read: - sys.stderr.write('Warning: No \"pair coeffs\" set.\n' - ' (No interactions between non-bonded atoms defined.)\n') - no_warnings = False - - #sys.stderr.write('Writing ttree data to standard out.\n' - # ' You can redirect this to a file using:\n'+ - # ' '+' '.join(sys.argv)+' > filename.ttree\n' - # ' ----------------------\n') - - if mol_name != '': - sys.stdout.write(mol_name + ' {\n') - - if len(l_in_init) > 0: - sys.stdout.write('\n### LAMMPS commands for initialization\n' - '### (These can be overridden later.)\n\n') - l_in_init.insert(0, (' '*cindent)+'write_once(\"'+in_init+'\") {\n') - l_in_init.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_init)) - if len(l_in_settings) > 0: - sys.stdout.write('\n### LAMMPS commands for settings\n' - '### (These can be overridden later.)\n\n') - l_in_settings.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_settings.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_settings)) - non_empty_output = True - if len(l_in_masses) > 0: - l_in_masses.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_masses.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_masses)) - non_empty_output = True - if len(l_in_pair_coeffs) > 0: - l_in_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_pair_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_pair_coeffs)) - non_empty_output = True - if len(l_in_bond_coeffs) > 0: - l_in_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_bond_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_bond_coeffs)) - non_empty_output = True - if len(l_in_angle_coeffs) > 0: - l_in_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_angle_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_angle_coeffs)) - non_empty_output = True - if len(l_in_dihedral_coeffs) > 0: - l_in_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_dihedral_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_dihedral_coeffs)) - non_empty_output = True - if len(l_in_improper_coeffs) > 0: - l_in_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+in_settings+'\") {\n') - l_in_improper_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_in_improper_coeffs)) - non_empty_output = True - - if non_empty_output: - sys.stdout.write('\n### DATA sections\n\n') - - if len(l_data_masses) > 0: - l_data_masses.insert(0, (' '*cindent)+'write_once(\"'+data_masses+'\") {\n') - l_data_masses.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_masses)) - non_empty_output = True - if len(l_data_bond_coeffs) > 0: - l_data_bond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bond_coeffs+'\") {\n') - l_data_bond_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bond_coeffs)) - non_empty_output = True - if len(l_data_angle_coeffs) > 0: - l_data_angle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angle_coeffs+'\") {\n') - l_data_angle_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angle_coeffs)) - non_empty_output = True - if len(l_data_dihedral_coeffs) > 0: - l_data_dihedral_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_dihedral_coeffs+'\") {\n') - l_data_dihedral_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedral_coeffs)) - non_empty_output = True - if len(l_data_improper_coeffs) > 0: - l_data_improper_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_improper_coeffs+'\") {\n') - l_data_improper_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_improper_coeffs)) - non_empty_output = True - if len(l_data_pair_coeffs) > 0: - l_data_pair_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_pair_coeffs+'\") {\n') - l_data_pair_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_pair_coeffs)) - non_empty_output = True - - # class2 force fields: - if len(l_data_bondbond_coeffs) > 0: - l_data_bondbond_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond_coeffs+'\") {\n') - l_data_bondbond_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondbond_coeffs)) - non_empty_output = True - if len(l_data_bondangle_coeffs) > 0: - l_data_bondangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondangle_coeffs+'\") {\n') - l_data_bondangle_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondangle_coeffs)) - non_empty_output = True - if len(l_data_middlebondtorsion_coeffs) > 0: - l_data_middlebondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_middlebondtorsion_coeffs+'\") {\n') - l_data_middlebondtorsion_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_middlebondtorsion_coeffs)) - non_empty_output = True - if len(l_data_endbondtorsion_coeffs) > 0: - l_data_endbondtorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_endbondtorsion_coeffs+'\") {\n') - l_data_endbondtorsion_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_endbondtorsion_coeffs)) - non_empty_output = True - if len(l_data_angletorsion_coeffs) > 0: - l_data_angletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angletorsion_coeffs+'\") {\n') - l_data_angletorsion_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angletorsion_coeffs)) - non_empty_output = True - if len(l_data_angleangletorsion_coeffs) > 0: - l_data_angleangletorsion_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangletorsion_coeffs+'\") {\n') - l_data_angleangletorsion_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angleangletorsion_coeffs)) - non_empty_output = True - if len(l_data_bondbond13_coeffs) > 0: - l_data_bondbond13_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_bondbond13_coeffs+'\") {\n') - l_data_bondbond13_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bondbond13_coeffs)) - non_empty_output = True - if len(l_data_angleangle_coeffs) > 0: - l_data_angleangle_coeffs.insert(0, (' '*cindent)+'write_once(\"'+data_angleangle_coeffs+'\") {\n') - l_data_angleangle_coeffs.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angleangle_coeffs)) - non_empty_output = True - - # automatic generation of bonded interactions by type: - if len(l_data_angles_by_type) > 0: - l_data_angles_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_angles_by_type+'\") {\n') - l_data_angles_by_type.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angles_by_type)) - non_empty_output = True - if len(l_data_dihedrals_by_type) > 0: - l_data_dihedrals_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_dihedrals_by_type+'\") {\n') - l_data_dihedrals_by_type.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedrals_by_type)) - non_empty_output = True - if len(l_data_impropers_by_type) > 0: - l_data_impropers_by_type.insert(0, (' '*cindent)+'write_once(\"'+data_impropers_by_type+'\") {\n') - l_data_impropers_by_type.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_impropers_by_type)) - non_empty_output = True - - if len(l_data_atoms) > 0: - l_data_atoms.insert(0, (' '*cindent)+'write(\"'+data_atoms+'\") {\n') - l_data_atoms.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_atoms)) - non_empty_output = True - else: - sys.stderr.write('Warning: missing \"Atoms\" section.\n' - ' (Did you include a LAMMPS data file in your argument list?)\n') - no_warnings = False - - # non-point-like particles - if len(l_data_ellipsoids) > 0: - l_data_ellipsoids.insert(0, (' '*cindent)+'write(\"'+data_ellipsoids+'\") {\n') - l_data_ellipsoids.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_ellipsoids)) - if len(l_data_lines) > 0: - l_data_lines.insert(0, (' '*cindent)+'write(\"'+data_lines+'\") {\n') - l_data_lines.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_lines)) - if len(l_data_triangles) > 0: - l_data_triangles.insert(0, (' '*cindent)+'write(\"'+data_triangles+'\") {\n') - l_data_triangles.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_triangles)) - - if len(l_data_velocities) > 0: - l_data_velocities.insert(0, (' '*cindent)+'write(\"'+data_velocities+'\") {\n') - l_data_velocities.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_velocities)) - if len(l_data_bonds) > 0: - l_data_bonds.insert(0, (' '*cindent)+'write(\"'+data_bonds+'\") {\n') - l_data_bonds.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_bonds)) - non_empty_output = True - if len(l_data_angles) > 0: - l_data_angles.insert(0, (' '*cindent)+'write(\"'+data_angles+'\") {\n') - l_data_angles.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_angles)) - non_empty_output = True - if len(l_data_dihedrals) > 0: - l_data_dihedrals.insert(0, (' '*cindent)+'write(\"'+data_dihedrals+'\") {\n') - l_data_dihedrals.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_dihedrals)) - non_empty_output = True - if len(l_data_impropers) > 0: - l_data_impropers.insert(0, (' '*cindent)+'write(\"'+data_impropers+'\") {\n') - l_data_impropers.append((' '*cindent)+'}\n') - sys.stdout.write('\n') - sys.stdout.write(''.join(l_data_impropers)) - non_empty_output = True - - if mol_name != '': - sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\n') - - if non_empty_output and no_warnings: - sys.stderr.write('WARNING: The '+g_program_name+' script has not been rigorously tested.\n' - ' Exotic (manybody) pair styles (and other force-field styles\n' - ' with unusual syntax) are not understood by '+g_program_name+'\n' - ' (although they are supported by moltemplate). Please look over\n' - ' the resulting LT file and check for errors. Convert any remaining\n' - ' atom, bond, angle, dihedral, or improper id or type numbers to the\n' - ' corresponding variables. Feel free to report any bugs you find.\n' - ' (-Andrew Jewett 2012-12-11)\n') - -except (ValueError, InputError) as err: - sys.stderr.write('\n'+str(err)+'\n') - sys.exit(-1) diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py deleted file mode 100755 index 1c7a655283..0000000000 --- a/tools/moltemplate/src/lttree.py +++ /dev/null @@ -1,745 +0,0 @@ -#!/usr/bin/env python - -# Author: Andrew Jewett (jewett.aij at g mail) -# http://www.chem.ucsb.edu/~sheagroup -# License: 3-clause BSD License (See LICENSE.TXT) -# Copyright (c) 2011, Regents of the University of California -# All rights reserved. - -""" -lttree.py - -lttree.py is an extension of the generic ttree.py program. -This version can understand and manipulate ttree-style templates which -are specialized for storing molecule-specific data for use in LAMMPS. - -The main difference between lttree.py and ttree.py is: -Unlike ttree.py, lttree.py understands rigid-body movement commands like -"rot()" and "move()" which allows it to reorient and move each copy -of a molecule to a new location. (ttree.py just ignores these commands. -Consequently LAMMPS input file (fragments) created with ttree.py have -invalid (overlapping) atomic coordinates and must be modified or aguemted -later (by loading atomic coordinates from a PDB file or an XYZ file). -lttree.py understands the "Data Atoms" section of a LAMMPS -data file (in addition to the various "atom_styles" which effect it). - -Additional LAMMPS-specific features may be added in the future. - -""" - -import sys -from ttree import * -from lttree_styles import * -from ttree_matrix_stack import * - -try: - unicode -except NameError: - # Python 3 - basestring = unicode = str - - - - -class LttreeSettings(BasicUISettings): - def __init__(self, - user_bindings_x=None, - user_bindings=None, - order_method='by_command'): - - BasicUISettings.__init__(self, - user_bindings_x, - user_bindings, - order_method) - - # The following new member data indicate which columns store - # LAMMPS-specific information. - # The next 6 members store keep track of the different columns - # of the "Data Atoms" section of a LAMMPS data file: - self.column_names = [] #<--A list of column names (optional) - self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data - self.ii_vects=[] #<--A list of triplets of column indexes storing directional data - # (such as dipole or ellipsoid orientations) - self.i_atomid=None #<--An integer indicating which column has the atomid - self.i_atomtype=None #<--An integer indicating which column has the atomtype - self.i_molid=None #<--An integer indicating which column has the molid, if applicable - self.infile=None # Name of the outermost file. This is the file - # which was read at the moment parsing begins. - - - - -def LttreeParseArgs(argv, settings): - - BasicUIParseArgs(argv, settings) - - # Loop over the remaining arguments not processed yet. - # These arguments are specific to the lttree.py program - # and are not understood by ttree.py: - i = 1 - while i < len(argv): - #sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n') - if ((argv[i].lower() == '-atomstyle') or - (argv[i].lower() == '-atom-style') or - (argv[i].lower() == '-atom_style')): - if i+1 >= len(argv): - raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n' - ' atom_style name (or single quoted string containing a space-separated\n' - ' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n') - settings.column_names = AtomStyle2ColNames(argv[i+1]) - sys.stderr.write('\n \"'+data_atoms+'\" column format:\n') - sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n') - settings.ii_coords = ColNames2Coords(settings.column_names) - settings.ii_vects = ColNames2Vects(settings.column_names) - settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) - del(argv[i:i+2]) - elif (argv[i].lower() == '-icoord'): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' - ' corresponding to column numbers for coordinates in\n' - ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') - ilist = argv[i+1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' - ' This is usually a list of 3 integers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - settings.iaffinevects = [] - for i in range(0, len(ilist)/3): - cols = [int(ilist[3*i])+1, - int(ilist[3*i+1])+1, - int(ilist[3*i+2])+1] - settings.iaffinevects.append(cols) - del(argv[i:i+2]) - elif (argv[i].lower() == '-ivect'): - if i+1 >= len(argv): - raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n' - ' corresponding to column numbers for direction vectors in\n' - ' the \"'+data_atoms+'\" section of a LAMMPS data file.\n') - ilist = argv[i+1].split() - if (len(ilist) % 3) != 0: - raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n' - ' This is usually a list of 3 integers, but it can contain more.\n' - ' The number of cooridnate columns must be divisible by 3,\n' - ' (even if the simulation is in 2 dimensions)\n') - settings.ivects = [] - for i in range(0, len(ilist)/3): - cols = [int(ilist[3*i])+1, - int(ilist[3*i+1])+1, - int(ilist[3*i+2])+1] - settings.ivects.append(cols) - del(argv[i:i+2]) - elif ((argv[i].lower() == '-iatomid') or - (argv[i].lower() == '-iid') or - (argv[i].lower() == '-iatom-id')): - if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): - raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' - ' LAMMPS data file contains the atom id number (typically 1).\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomid = int(argv[i+1])-1 - del(argv[i:i+2]) - elif ((argv[i].lower() == '-iatomtype') or - (argv[i].lower() == '-itype') or - (argv[i].lower() == '-iatom-type')): - if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): - raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' - ' LAMMPS data file contains the atom type.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_atomtype = int(argv[i+1])-1 - del(argv[i:i+2]) - elif ((argv[i].lower() == '-imolid') or - (argv[i].lower() == '-imol') or - (argv[i].lower() == '-imol-id') or - (argv[i].lower() == '-imoleculeid') or - (argv[i].lower() == '-imolecule-id')): - if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))): - raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n' - ' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n' - ' LAMMPS data file contains the molecule id number.\n' - ' (This argument is unnecessary if you use the -atomstyle argument.)\n') - i_molid = int(argv[i+1])-1 - del(argv[i:i+2]) - - elif ((argv[i][0] == '-') and (__name__ == "__main__")): - #elif (__name__ == "__main__"): - raise InputError('Error('+g_program_name+'):\n' - 'Unrecogized command line argument \"'+argv[i]+'\"\n') - else: - i += 1 - - - if __name__ == "__main__": - - # Instantiate the lexer we will be using. - # (The lexer's __init__() function requires an openned file. - # Assuming __name__ == "__main__", then the name of that file should - # be the last remaining (unprocessed) argument in the argument list. - # Otherwise, then name of that file will be determined later by the - # python script which imports this module, so we let them handle it.) - - if len(argv) == 1: - raise InputError('Error: This program requires at least one argument\n' - ' the name of a file containing ttree template commands\n') - elif len(argv) == 2: - try: - settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file - except IOError: - sys.stderr.write('Error: unable to open file\n' - ' \"'+argv[1]+'\"\n' - ' for reading.\n') - sys.exit(1) - del(argv[1:2]) - - else: - # if there are more than 2 remaining arguments, - problem_args = ['\"'+arg+'\"' for arg in argv[1:]] - raise InputError('Syntax Error('+g_program_name+'):\n\n' - ' Problem with argument list.\n' - ' The remaining arguments are:\n\n' - ' '+(' '.join(problem_args))+'\n\n' - ' (The actual problem may be earlier in the argument list.\n' - ' If these arguments are source files, then keep in mind\n' - ' that this program can not parse multiple source files.)\n' - ' Check the syntax of the entire argument list.\n') - - - - if len(settings.ii_coords) == 0: - sys.stderr.write('########################################################\n' - '## WARNING: atom_style unspecified ##\n' - '## --> \"'+data_atoms+'\" column data has an unknown format ##\n' - '## Assuming atom_style = \"full\" ##\n' - # '########################################################\n' - # '## To specify the \"'+data_atoms+'\" column format you can: ##\n' - # '## 1) Use the -atomstyle \"STYLE\" argument ##\n' - # '## where \"STYLE\" is a string indicating a LAMMPS ##\n' - # '## atom_style, including hybrid styles.(Standard ##\n' - # '## atom styles defined in 2011 are supported.) ##\n' - # '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n' - # '## where \"COL_LIST" is a quoted list of strings ##\n' - # '## indicating the name of each column. ##\n' - # '## Names \"x\",\"y\",\"z\" are interpreted as ##\n' - # '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n' - # '## are interpreted as direction vectors. ##\n' - # '## 3) Use the -icoord \"cx cy cz...\" argument ##\n' - # '## where \"cx cy cz\" is a list of integers ##\n' - # '## indicating the column numbers for the x,y,z ##\n' - # '## coordinates of each atom. ##\n' - # '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n' - # '## where \"cmux cmuy cmuz...\" is a list of ##\n' - # '## integers indicating the column numbers for ##\n' - # '## the vector that determines the direction of a ##\n' - # '## dipole or ellipsoid (ie. a rotateable vector).##\n' - # '## (More than one triplet can be specified. The ##\n' - # '## number of entries must be divisible by 3.) ##\n' - '########################################################\n') - - # The default atom_style is "full" - settings.column_names = AtomStyle2ColNames('full') - settings.ii_coords = ColNames2Coords(settings.column_names) - settings.ii_vects = ColNames2Vects(settings.column_names) - settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names) - - - - - - - - - -def TransformAtomText(text, matrix): - """ Apply transformations to the coordinates and other vector degrees - of freedom stored in the \"Data Atoms\" section of a LAMMPS data file. - This is the \"text\" argument. - The \"matrix\" stores the aggregate sum of combined transformations - to be applied. - - """ - - #sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n') - - lines = text.split('\n') - - for i in range(0, len(lines)): - line_orig = lines[i] - ic = line_orig.find('#') - if ic != -1: - line = line_orig[:ic] - comment = ' '+line_orig[ic:].rstrip('\n') - else: - line = line_orig.rstrip('\n') - comment = '' - - columns = line.split() - if len(columns) > 0: - if len(columns) == len(settings.column_names)+3: - raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n' - ' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n' - ' Instead please add the appropriate offsets (these offsets\n' - ' should be multiples of the cell size) to the atom coordinates\n' - ' in the data file, and eliminate the extra columns. Then try again.\n' - ' (If you get this message often, email me and I\'ll fix this limitation.)') - if len(columns) < len(settings.column_names): - raise InputError('Error: The number of columns in your data file does not\n' - ' match the LAMMPS atom_style you selected.\n' - ' Use the -atomstyle