diff --git a/tools/moltemplate/LICENSE.TXT b/tools/moltemplate/LICENSE.TXT deleted file mode 100644 index 86812ab329..0000000000 --- a/tools/moltemplate/LICENSE.TXT +++ /dev/null @@ -1,28 +0,0 @@ - -Author: Andrew Jewett, Shea Group, http://www.chem.ucsb.edu/~sheagroup/ -Copyright (c) 2012, Regents of the University of California -All rights reserved. -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - - * Redistributions of source code must retain the above copyright notice, - this list of conditions and the following disclaimer. - * Redistributions in binary form must reproduce the above copyright notice, - this list of conditions and the following disclaimer in the documentation - and/or other materials provided with the distribution. - * Neither the name of the University of California, Santa Barbara nor the - names of its contributors may be used to endorse or promote products - derived from this software without specific prior written permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE -LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF -THE POSSIBILITY OF SUCH DAMAGE. - diff --git a/tools/moltemplate/README.TXT b/tools/moltemplate/README.TXT deleted file mode 100644 index 34d4713064..0000000000 --- a/tools/moltemplate/README.TXT +++ /dev/null @@ -1,65 +0,0 @@ -Moltemplate tool - - -- Description: -- - -Moltemplate is a cross-platform text-based molecule builder for LAMMPS. - - -- Typical usage: -- - -moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] file.lt - - -- Web page: -- - -Documentation, examples, and supporting code can be downloaded at: - - http://www.moltemplate.org -The most up-to-date version of moltemplate can be downloaded here. -(After download, you can unpack the archive using: - tar xzf moltemplate_2012-3-31.tar.gz -The date will vary from version to version.) - ----------------------------------------------------- ----------- INSTALLATION INSTRUCTIONS: ------------ ----------------------------------------------------- - -This directory should contain 4 sub-directories: - src/ <-- location of all python and bash scripts - common/ <-- location of shared force fields and molecules - doc/ <-- moltemplate manual as PDF file - examples/ <-- various examples, see examples/README.TXT - -The ``moltemplate.sh'' script and the python scripts that it invokes -are located in the ``src/'' subdirectory. You should update your PATH -environment variable to include this directory. - -If you do not know what a PATH environment variable is, read: - http://www.linfo.org/path_env_var.html -(I receive this question often.) - -It is also a good idea to set your MOLTEMPLATE_PATH environment -variable to point to the ``common/'' subdirectory. (Force fields and -commonly used molecules will eventually be located here.) - - -- Installation example --- - -Suppose the directory with this README.TXT file is located at ~/moltemplate. - -If you use the bash shell, typically you would edit your -~/.profile, ~/.bash_profile or ~/.bashrc files to contain the following lines: - export PATH="$PATH:$HOME/moltemplate/src" - export MOLTEMPLATE_PATH="$HOME/moltemplate/common" -If you use the tcsh shell, typically you would edit your -~/.login, ~/.cshrc, or ~/.tcshrc files to contain the following lines: - setenv PATH "$PATH:$HOME/moltemplate/src" - setenv MOLTEMPLATE_PATH "$HOME/moltemplate/common" - - -- Requirements: -- - -Moltemplate requires the Bourne-shell, and a recent version of python -(2.7, 3.0 or higher), and can run on OS X, linux, or windows (if a -suitable shell environment has been installed). - - -- License: -- - -Moltemplate is available under the terms of the open-source 3-clause -BSD license (See LICENSE.TXT.) diff --git a/tools/moltemplate/common/same_files_with_comments/trappe1998_with_comments.lt b/tools/moltemplate/common/same_files_with_comments/trappe1998_with_comments.lt deleted file mode 100644 index 7a6807f9b9..0000000000 --- a/tools/moltemplate/common/same_files_with_comments/trappe1998_with_comments.lt +++ /dev/null @@ -1,123 +0,0 @@ -# This file contains force field parameters for the "TraPPE" potential used -# to model conformational change and interactions between coarse-grained -# alkane chains. This is a united-atom model. (Hydrogens are not represented -# explicitly.) This model is described in more detail here: -# -# Martin, M.G. and Siepmann. J.I. -# "Transferable potentials for phase equilibria. 1. united-atom description -# of n-alkanes." J. Phys. Chem. B, 102(14):2569–2577, 1998. -# -# ---- Force-Field File Format explanation ---- -# -# Lammps-template files (LT files) contain object defintions like this: -# -# OBJECT_NAME { -# write commands { text and @ and $ variables...} -# } -# -# Often these objects are definitions of molecules -# which can be copied or pasted together to build larger molecules. -# -# However this file defines the static "TraPPE" object. -# "TraPPE" is not a molecule, but a collection of atom types, -# and a description of the interactions between them. -# These atoms can then be used inside other molecules. -# So you can think of the "TraPPE" object as an environment (namespace) -# describing the interactions between a limited set of atoms. -# Later on whenever you build a new molecule using TraPPE atoms, -# (for example using this syntax "@atom:.../TraPPE/CH2"), -# then the forces between them will be generated automatically. -# -# The dihedral (torsion) angle forces are given by -# U_dihedral(x) = -# = 0.5*(1.411036*(1+cos(x)) - 0.271016*(1-cos(2*x)) + 3.145034*(1+cos(3*x))) -# Note: The TraPPE authors suggest using bond-constraints like "SHAKE". -# Unfortunatley, in LAMMPS, SHAKE does not work for large molecules. -# Units: -# Energies in this file are in kCal/mole. (Where k_B = 0.001987207 in units of -# kCal mole^(-1) Kelvin^(-1), and 1 "thermochemical" calorie = 4.184000 Joule) - -TraPPE { - - write_once("Data Masses") { - @atom:CH2 14.1707 - @atom:CH3 15.2507 - @atom:CH4 16.3307 - } - # The "atoms" named "CH2", "CH3", "CH4" denote carbon atoms - # bonded to 2, 3, and 4 hydrogen atoms, respectively. - - # The following two "write_once()" statements instruct moltemplate.sh - # to automatically generate a 3-body "angle" or 4-body "dihedral" - # ineractions between any time 3 or 4 carbon atoms which are connected - # by consecutive "saturated". All three types of carbon atoms above - # have a name which matches "CH?". ('?' and '*' are wildcard characters.) - # Parameters for these "backbone" interactions are defined below. - - 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 - } - - # Force-field parameters: - - write_once("In Settings") { - - # -- Default settings/parameters for "TraPPE" -- - # (Hybrid styles were used for portability.) - - 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 - # (Interactions between different atom types in this list use mixing rules.) - - 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 - - } - - - # ------------------------------------------------------------------ - # --------------- OPTIONAL DEFAULT SETTINGS BELOW ----------------- - # ------------------------------------------------------------------ - # -- All settings below are optional and can be overridden later. -- - # -- They are only suggestions how to run LAMMPS with this model. -- - # ------------------------------------------------------------------ - - - # ------ lammps input script suggestions: ------ - # Style suggestions: - - 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 - } - - # Here's an example of how define a LAMMPS group for all TraPPE atoms - # Note we have to list them all explicitly (CH2, CH3, CH4, not CH*). - # (Wildcards like '*' and '?' only work for "By Type" interactions, not here.) - - write_once("In Settings") { - # -- Optional "TraPPE" groups -- - group TraPPE type @atom:CH2 @atom:CH3 @atom:CH4 - # (Atoms types between @{atom:CH2}-@{atom:CH4} belong to the "TraPPE" group. - # Note: All included atom types should explicitly appear in above list.) - } - -} # class TraPPE - - diff --git a/tools/moltemplate/common/same_files_with_comments/watmw_with_comments.lt b/tools/moltemplate/common/same_files_with_comments/watmw_with_comments.lt deleted file mode 100644 index b5fb71e25c..0000000000 --- a/tools/moltemplate/common/same_files_with_comments/watmw_with_comments.lt +++ /dev/null @@ -1,62 +0,0 @@ -# This file contains the defintion of the "WatMW" water -# molecule model, as defined in this paper: -# Molinero, V. and Moore, E.B., J. Phys. Chem. B 2009, 113, 4008-4016 -# (In that paper, they call it the "mW" water model.) -# -# Each "WatMW" molecule below contains only a single particle (type "@atom:mW"). -# These particles interact via 3-body Stillinger-Weber potentials. - -WatMW { - # atom-id mol-id atom-type charge x y z - write("Data Atoms") { - $atom:mW $mol:. @atom:mW 0.0 0.0 0.0 0.0 - } - - write_once("Data Masses") { - @atom:mW 18.02 - } - - # Stillinger-Weber parameters for the "mW" model - 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 - } -} - - - - - - - - - -# ---------- OPTIONAL DEFAULT SETTINGS ------------- - - # ------------------------------------------------------------------------- - # ---- All settings below are optional and can be overridden later. ---- - # ---- They are only suggestions how to run LAMMPS with this model. ---- - # ------------------------------------------------------------------------- - -WatMW { # <-- Append additional content to the "WatMW" class defined above - - write_once("In Init") { - # -- Default styles for "WatMW" -- - units real - pair_style sw - } - - write_once("In Settings") { - # -- Optional: Define the group of "mW" water molecules -- - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - - write_once("In Settings") { - # -- Default WatMW pair_coeffs were not supplied here because many-body -- - # -- pair-styles like "sw" have pair_coeffs which can not be over-ridden -- - # -- later. You must figure out the number of atom types beforehand. -- - # -- Here is what you would use if only mW water is present: -- - # -- pair_coeff * * system.in.sw mW -- - } - -} # suggested WatMW style settings - diff --git a/tools/moltemplate/common/spce.lt b/tools/moltemplate/common/spce.lt deleted file mode 100644 index 7ed9567d45..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 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 all 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/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 4728623c28..0000000000 --- a/tools/moltemplate/common/watmw.lt +++ /dev/null @@ -1,33 +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") { - group WatMW type @atom:mW #(Atoms of this type belong to the "WatMW" group) - } - -} # WatMW diff --git a/tools/moltemplate/doc/moltemplate_manual.pdf b/tools/moltemplate/doc/moltemplate_manual.pdf deleted file mode 100644 index f4ac48f124..0000000000 --- a/tools/moltemplate/doc/moltemplate_manual.pdf +++ /dev/null @@ -1,9125 +0,0 @@ -%PDF-1.4 -% -1 0 obj -<< /S /GoTo /D (section.1) >> -endobj -4 0 obj -(Introduction) -endobj -5 0 obj -<< /S /GoTo /D (subsection.1.1) >> -endobj -8 0 obj -(Converting LT files to LAMMPS input/data files) -endobj -9 0 obj -<< /S /GoTo /D (subsection.1.2) >> -endobj -12 0 obj -(Converting LAMMPS input/data files to LT files) -endobj -13 0 obj -<< /S /GoTo /D (section.2) >> -endobj -16 0 obj -(Installation) -endobj -17 0 obj -<< /S /GoTo /D (section.3) >> -endobj -20 0 obj -(Quick reference \(skip on first reading\)) -endobj -21 0 obj -<< /S /GoTo /D (subsection.3.1) >> -endobj -24 0 obj -(Moltemplate commands) -endobj -25 0 obj -<< /S /GoTo /D (subsection.3.2) >> -endobj -28 0 obj -(Common \044 and @ variables) -endobj -29 0 obj -<< /S /GoTo /D (subsection.3.3) >> -endobj -32 0 obj -(Coordinate transformations) -endobj -33 0 obj -<< /S /GoTo /D (subsection.3.4) >> -endobj -36 0 obj -(moltemplate.sh command line arguments:) -endobj -37 0 obj -<< /S /GoTo /D (section.4) >> -endobj -40 0 obj -(Introductory tutorial) -endobj -41 0 obj -<< /S /GoTo /D (subsection.4.1) >> -endobj -44 0 obj -(Simulating a box of water using moltemplate and LAMMPS) -endobj -45 0 obj -<< /S /GoTo /D (subsection.4.2) >> -endobj -48 0 obj -(Coordinate generation) -endobj -49 0 obj -<< /S /GoTo /D (subsection.4.3) >> -endobj -52 0 obj -(Running a LAMMPS simulation \(after using moltemplate\)) -endobj -53 0 obj -<< /S /GoTo /D (section.5) >> -endobj -56 0 obj -(Overview) -endobj -57 0 obj -<< /S /GoTo /D (subsection.5.1) >> -endobj -60 0 obj -(Basics: The write\(\) and write\137once\(\) commands) -endobj -61 0 obj -<< /S /GoTo /D (subsection.5.2) >> -endobj -64 0 obj -(Basics: counter variables) -endobj -65 0 obj -<< /S /GoTo /D (subsubsection.5.2.1) >> -endobj -68 0 obj -(Static counters begin with ``@'') -endobj -69 0 obj -<< /S /GoTo /D (subsubsection.5.2.2) >> -endobj -72 0 obj 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(subsection.6.1) >> -endobj -108 0 obj -(Building a large molecule from smaller pieces) -endobj -109 0 obj -<< /S /GoTo /D (subsection.6.2) >> -endobj -112 0 obj -(Sharing atom, bond and angle types) -endobj -113 0 obj -<< /S /GoTo /D (subsection.6.3) >> -endobj -116 0 obj -(Bonded interactions by type) -endobj -117 0 obj -<< /S /GoTo /D (section.7) >> -endobj -120 0 obj -(Arrays and coordinate transformations) -endobj -121 0 obj -<< /S /GoTo /D (subsection.7.1) >> -endobj -124 0 obj -(Transformations following brackets [] in a new statement) -endobj -125 0 obj -<< /S /GoTo /D (subsection.7.2) >> -endobj -128 0 obj -(Transformations following instantiation) -endobj -129 0 obj -<< /S /GoTo /D (subsection.7.3) >> -endobj -132 0 obj -(Transformation order \(general case\)) -endobj -133 0 obj -<< /S /GoTo /D (subsection.7.4) >> -endobj -136 0 obj -(Random arrays) -endobj -137 0 obj -<< /S /GoTo /D (subsection.7.5) >> -endobj -140 0 obj -([*] and [i-j] notation) -endobj -141 0 obj -<< /S /GoTo /D (section.8) >> -endobj -144 0 obj -(Customizing molecule position and topology) -endobj -145 0 obj -<< /S /GoTo /D (subsection.8.1) >> -endobj -148 0 obj -(Customizing individual atom location) -endobj -149 0 obj -<< /S /GoTo /D (subsection.8.2) >> -endobj -152 0 obj -(Adding bonds and angles to individual molecules) -endobj -153 0 obj -<< /S /GoTo /D (subsection.8.3) >> -endobj -156 0 obj -(The delete command) -endobj -157 0 obj -<< /S /GoTo /D (subsubsection.8.3.1) >> -endobj -160 0 obj -(Deleting molecules or molecular subunits) -endobj -161 0 obj -<< /S /GoTo /D (subsubsection.8.3.2) >> -endobj -164 0 obj -(Deleting atoms, bonds, angles, dihedrals, and impropers) -endobj -165 0 obj -<< /S /GoTo /D (section.9) >> -endobj -168 0 obj -(Multidimensional arrays) -endobj -169 0 obj -<< /S /GoTo /D (subsection.9.1) >> -endobj -172 0 obj -(Customizing individual rows, columns, or layers) -endobj -173 0 obj -<< /S /GoTo /D (subsection.9.2) >> -endobj -176 0 obj -(Creating random 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00000 n -0000739197 00000 n -0000739310 00000 n -0000739431 00000 n -0000739555 00000 n -0000739655 00000 n -0000739766 00000 n -0000739804 00000 n -0000739932 00000 n -trailer -<< /Size 983 -/Root 981 0 R -/Info 982 0 R -/ID [<8C292AA6E6A7A3973D6F2BDE9D32B6A2> <8C292AA6E6A7A3973D6F2BDE9D32B6A2>] >> -startxref -740258 -%%EOF diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT deleted file mode 100644 index 0aeed79a5b..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README.TXT +++ /dev/null @@ -1,56 +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 new DLPC model is a truncated version of DPPC.) - The protein model is described here: - G. Bellesia, AI Jewett, and J-E Shea, - Protein Science, Vol19 141-154 (2010) - -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. - ------ 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. -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_membrane_examples/membrane+protein/README_run.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_run.sh deleted file mode 100755 index 18d5b65b6f..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_run.sh +++ /dev/null @@ -1,33 +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) -"$LAMMPS_COMMAND" -i run.in.npt # pressure equilibration -"$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.npt # pressure equilibration -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_setup.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_setup.sh deleted file mode 100755 index 4414a4a4b0..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/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 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 -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_membrane_examples/membrane+protein/README_visualise.txt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/README_visualise.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_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg deleted file mode 100644 index 246ee54625..0000000000 Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 78f8e6b841..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/images/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,2611 +0,0 @@ -PSF - 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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 - - # -------------- 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 class2 - 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 6.0 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") { - # Override any pair_coeff and bond_coeff - # statements from the 1beadProteSci2010 model - # (Because the energies &distances in that model - # were in the wrong units.) - pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 6.0 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 6.0 - } - - - # 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. Note: If you want the "AF" model, - # then change this to "delta60_0".) - - @dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * * - - # If tN atoms are present, use the @dihedral:turn parameters - @dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * * - @dihedral:turn @atom:tN @atom:tN @atom:* @atom:* * * * - @dihedral:turn @atom:tN @atom:tN @atom:tN @atom:* * * * - @dihedral:turn @atom:tN @atom:tN @atom:tN @atom:tN * * * - } - - write_once("In Settings") { - dihedral_coeff @dihedral:delta60_0 class2 2.167862 120.0 0 0 2.167862 180.0 - dihedral_coeff @dihedral:delta65_0 class2 2.167862 115.0 0 0 2.167862 180.0 - dihedral_coeff @dihedral:turn class2 0 0 0 0 0.361310 180.0 - # Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon. - - # 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:delta65_0 class2 mbt 0 0 0 0 - dihedral_coeff @dihedral:delta65_0 class2 ebt 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta65_0 class2 at 0 0 0 0 0 0 0 0 - dihedral_coeff @dihedral:delta65_0 class2 aat 0 0 0 - dihedral_coeff @dihedral:delta65_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 - } - - - # --- 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_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt deleted file mode 100644 index a04db1f62f..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/1beadProtSci2010_variations.lt +++ /dev/null @@ -1,208 +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 - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index bb9a732c1b..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,186 +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. - - - -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 - - # 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.) - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - # Optional: The "multi" style could be useful to efficiently simulate - # particles different sizes together. The tabular potential has range - # 22.5 Angstoms, but the Lennard-Jones forces have range of only - # 15.0 Angstroms. - - neighbor 2.0 multi - communicate multi - } - - - # 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 will override it later - } - - - - # All force-field parameters appear in the "In Settings" section, - # which is later included in the LAMMPS input script. - # These force-field parameters are shared between all lipids by default. - # These can be customized and overridden for specific lipid types later. - - - # 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. - - 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 popular. Using this convention makes it easier - # to mix this coarse-grained lipid model with other molecular models. - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # custom "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 # custom "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 - - - -} # CGLipidBr2005 - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py deleted file mode 100755 index ae4160531c..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/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 = 2.6 -Rmax = 22.6 -rcut = 22.5 -N = 1001 - -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_membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/calc_table/version_charmm_cutoff/calc_table.py deleted file mode 100755 index 48f199074c..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/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 = 2.6 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1001 - -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_membrane_examples/membrane+protein/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/system.lt deleted file mode 100644 index efb2442559..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/system.lt +++ /dev/null @@ -1,178 +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. -# (In the future moltemplate will be able to avoid occlusion automatically.) - - -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][*] - - -# -------- interactions between protein and lipids ---------- - -# 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 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. - - # i j pairstylename eps sig K L - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - - # We want the interactions between hydrophobic residues and atoms in - # the interior of the lipd to be energetically similar to the attractive - # interactions between hydrophobic residues. (See 1beadProtSci2010.) - - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - - # We also add an artificial attractive interaction between the - # turn residues of the protein and the lipid head groups in - # order to keep the protein upright. Probably not necessary. - - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1 - - # All other interactions between proteins and lipids are steric. - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 6.0 1 0 - - - # Add a weak attractive interaction between hydrophilic "sL" beads - # (Whose strength mimics the strength of interaction between tail beads - # in the lipid. This was absent from the original protein model. - # However without some kind of weak attraction between residues, - # the negative pressure in the interior of the bilayer membrane - # allways pulls the protein apart. Recall that in the membrane, - # the hydrophobic beads in the protein will face outwards towards the lipid - # tails leaving the hydrophilic amino acids of the protein in the interior. - # In reality, these polar groups form hydrogen bonds with each other.) - - pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 7.5 0.4 -1 - - # However these hydrophilic amino acids are not attrected to - # the bilayer interior. - - pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0 - -} - - - - -# 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 class2 - 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" -} - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat deleted file mode 100644 index 31b9f0c450..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1010 +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 1001 - -1 2.6 87252.0069441 402763.664479 -2 2.62 79585.4554502 364574.203947 -3 2.64 72643.2434671 330255.845328 -4 2.66 66352.2073932 299391.208536 -5 2.68 60647.0444312 271610.570248 -6 2.7 55469.4181565 246586.123584 -7 2.72 50767.1714483 224026.964698 -8 2.74 46493.633237 203674.709811 -9 2.76 42607.0073083 185299.659567 -10 2.78 39069.8329526 168697.439095 -11 2.8 35848.5085794 153686.051901 -12 2.82 32912.8705664 140103.294183 -13 2.84 30235.8206098 127804.483324 -14 2.86 27792.9956998 116660.460548 -15 2.88 25562.4755962 106555.833042 -16 2.9 23524.5233195 97387.4254387 -17 2.92 21661.3547409 89062.9145204 -18 2.94 19956.9338374 81499.6244039 -19 2.96 18396.7906059 74623.4624292 -20 2.98 16967.8589974 68367.9785194 -21 3.0 15658.3325568 62673.5329856 -22 3.02 14457.5357325 57486.5596649 -23 3.04 13355.809067 52758.912937 -24 3.06 12344.4066925 48447.2886046 -25 3.08 11415.4047444 44512.7098736 -26 3.1 10561.6194689 40920.0707567 -27 3.12 9776.5339459 37637.7301715 -28 3.14 9054.23247117 34637.1508274 -29 3.16 8389.34175838 31892.5777179 -30 3.18 7776.97821258 29380.7516608 -31 3.2 7212.7006167 27080.6538766 -32 3.22 6692.4676457 24973.2780793 -33 3.24 6212.59969004 23041.4269669 -34 3.26 5769.74452856 21269.5303734 -35 3.28 5360.84644195 19643.4826615 -36 3.3 4983.1184041 18150.4972204 -37 3.32 4634.01702836 16778.97618 -38 3.34 4311.21998136 15518.393672 -39 3.36 4012.60560869 14359.191159 -40 3.38 3736.23454428 13292.6835236 -41 3.4 3480.33310029 12310.9747549 -42 3.42 3243.27825585 11406.8822043 -43 3.44 3023.58408279 10573.8684961 -44 3.46 2819.88946345 9805.98028003 -45 3.48 2630.94697101 9097.79310596 -46 3.5 2455.61279669 8444.36177626 -47 3.52 2292.83761972 7841.17560602 -48 3.54 2141.65832756 7284.11808108 -49 3.56 2001.19050257 6769.43046025 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-0.000781053201174 -0.0195785060596 -995 22.48 -0.000390005459079 -0.019526299124 -996 22.5 0.0 -0.0194742776206 -997 22.52 0.0 0.0 -998 22.54 0.0 0.0 -999 22.56 0.0 0.0 -1000 22.58 0.0 0.0 -1001 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.min b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/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_membrane_examples/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt deleted file mode 100644 index af4890aa02..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.npt +++ /dev/null @@ -1,60 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the CLASS2 package. -# 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-class2" 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 -- - - -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 - -# 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 - - -#restart 1000000 - -run 2000000 - -write_restart system_after_npt.rst - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt deleted file mode 100644 index 54c3d61823..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane+protein/run.in.nvt +++ /dev/null @@ -1,40 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# read_data system.data <-- commenting out -# Use the pressure-equilibrated restart file instead: -read_restart system_after_npt.rst - - -# -- 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 20000 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 20000000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README.TXT b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README.TXT deleted file mode 100644 index 295af3fd16..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/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_membrane_examples/membrane_BranniganPRE2005/README_run.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_run.sh deleted file mode 100755 index 18d5b65b6f..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_run.sh +++ /dev/null @@ -1,33 +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.npt # pressure equilibration -"$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.npt # pressure equilibration -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_setup.sh b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_setup.sh deleted file mode 100755 index 4414a4a4b0..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/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 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 -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_membrane_examples/membrane_BranniganPRE2005/README_visualise.txt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/README_visualise.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_membrane_examples/membrane_BranniganPRE2005/images/DLPC.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DLPC.jpg deleted file mode 100644 index 637f2f1c7a..0000000000 Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DLPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg deleted file mode 100644 index 14f1a1ed2c..0000000000 Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/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_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg deleted file mode 100644 index 2322449c1d..0000000000 Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC.jpg b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC.jpg deleted file mode 100644 index 57e093023d..0000000000 Binary files a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/images/DPPC.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt deleted file mode 100644 index bb9a732c1b..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/CGLipidBr2005.lt +++ /dev/null @@ -1,186 +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. - - - -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 - - # 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.) - - pair_modify mix arithmetic - special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds" - - # Optional: The "multi" style could be useful to efficiently simulate - # particles different sizes together. The tabular potential has range - # 22.5 Angstoms, but the Lennard-Jones forces have range of only - # 15.0 Angstroms. - - neighbor 2.0 multi - communicate multi - } - - - # 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 will override it later - } - - - - # All force-field parameters appear in the "In Settings" section, - # which is later included in the LAMMPS input script. - # These force-field parameters are shared between all lipids by default. - # These can be customized and overridden for specific lipid types later. - - - # 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. - - 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 popular. Using this convention makes it easier - # to mix this coarse-grained lipid model with other molecular models. - - - DPPC { - write("Data Atoms") { - $atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # custom "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 # custom "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 - - - -} # CGLipidBr2005 - diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/calc_table.py deleted file mode 100755 index ae4160531c..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/generate_tables/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 = 2.6 -Rmax = 22.6 -rcut = 22.5 -N = 1001 - -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_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt deleted file mode 100644 index 81aefe6ff8..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/system.lt +++ /dev/null @@ -1,90 +0,0 @@ -# Description: - -# This example shows how to build a lipid bilayer composed of a -# 50%-50% mixture of two different lipids (DPPC and DLPC). -# The DPPC model is described here: -# G. Brannigan, P.F. Philips, and F.L.H. Brown, -# Physical Review E, Vol 72, 011915 (2005) -# The new DLPC model is a truncated version of DPPC, -# (Its behaviour has not been rigorously tested.) -# Note: 50%/50% mixtures of DPPC & DLPC are commonly used to build liposomes -# http://www.ncbi.nlm.nih.gov/pubmed/10620293 - - -import "CGLipidBr2005.lt" - -using namespace CGLipidBr2005 - -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) - -# 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. - - -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) The example we use here is a lipid mixture of DPPC and DLPC, so we 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_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat deleted file mode 100644 index 31b9f0c450..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/table_int.dat +++ /dev/null @@ -1,1010 +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 1001 - -1 2.6 87252.0069441 402763.664479 -2 2.62 79585.4554502 364574.203947 -3 2.64 72643.2434671 330255.845328 -4 2.66 66352.2073932 299391.208536 -5 2.68 60647.0444312 271610.570248 -6 2.7 55469.4181565 246586.123584 -7 2.72 50767.1714483 224026.964698 -8 2.74 46493.633237 203674.709811 -9 2.76 42607.0073083 185299.659567 -10 2.78 39069.8329526 168697.439095 -11 2.8 35848.5085794 153686.051901 -12 2.82 32912.8705664 140103.294183 -13 2.84 30235.8206098 127804.483324 -14 2.86 27792.9956998 116660.460548 -15 2.88 25562.4755962 106555.833042 -16 2.9 23524.5233195 97387.4254387 -17 2.92 21661.3547409 89062.9145204 -18 2.94 19956.9338374 81499.6244039 -19 2.96 18396.7906059 74623.4624292 -20 2.98 16967.8589974 68367.9785194 -21 3.0 15658.3325568 62673.5329856 -22 3.02 14457.5357325 57486.5596649 -23 3.04 13355.809067 52758.912937 -24 3.06 12344.4066925 48447.2886046 -25 3.08 11415.4047444 44512.7098736 -26 3.1 10561.6194689 40920.0707567 -27 3.12 9776.5339459 37637.7301715 -28 3.14 9054.23247117 34637.1508274 -29 3.16 8389.34175838 31892.5777179 -30 3.18 7776.97821258 29380.7516608 -31 3.2 7212.7006167 27080.6538766 -32 3.22 6692.4676457 24973.2780793 -33 3.24 6212.59969004 23041.4269669 -34 3.26 5769.74452856 21269.5303734 -35 3.28 5360.84644195 19643.4826615 -36 3.3 4983.1184041 18150.4972204 -37 3.32 4634.01702836 16778.97618 -38 3.34 4311.21998136 15518.393672 -39 3.36 4012.60560869 14359.191159 -40 3.38 3736.23454428 13292.6835236 -41 3.4 3480.33310029 12310.9747549 -42 3.42 3243.27825585 11406.8822043 -43 3.44 3023.58408279 10573.8684961 -44 3.46 2819.88946345 9805.98028003 -45 3.48 2630.94697101 9097.79310596 -46 3.5 2455.61279669 8444.36177626 -47 3.52 2292.83761972 7841.17560602 -48 3.54 2141.65832756 7284.11808108 -49 3.56 2001.19050257 6769.43046025 -50 3.58 1870.62160083 6293.67891689 -51 3.6 1749.20475558 5853.72485855 -52 3.62 1636.25314534 5446.69810179 -53 3.64 1531.13487237 5069.97261409 -54 3.66 1433.26830277 4721.1445646 -55 3.68 1342.11782445 4398.01245332 -56 3.7 1257.18998347 4098.55911171 -57 3.72 1178.02996319 3820.93539003 -58 3.74 1104.21837425 3563.44536511 -59 3.76 1035.36832639 3324.53291993 -60 3.78 971.122756088 3102.76956138 -61 3.8 911.151986554 2896.84335615 -62 3.82 855.151498616 2705.54887715 -63 3.84 802.83989347 2527.77806329 -64 3.86 753.957029799 2362.51190574 -65 3.88 708.262319576 2208.81288195 -66 3.9 665.533168297 2065.81806693 -67 3.92 625.563546756 1932.73285812 -68 3.94 588.162682667 1808.82525631 -69 3.96 553.153861545 1693.42065104 -70 3.98 520.373327227 1585.89706361 -71 4.0 489.669273313 1485.68080556 -72 4.02 460.900917596 1392.24251449 -73 4.04 433.937652306 1305.09353282 -74 4.06 408.6582636 1223.78259822 -75 4.08 384.950214367 1147.89281764 -76 4.1 362.708984933 1077.03889938 -77 4.12 341.837466738 1010.86461999 -78 4.14 322.245404503 949.040505266 -79 4.16 303.848882793 891.261706073 -80 4.18 286.569853265 837.246052066 -81 4.2 270.33569919 786.732267446 -82 4.22 255.078834164 739.47833469 -83 4.24 240.736332164 695.259993326 -84 4.26 227.249586386 653.869362042 -85 4.28 214.563994495 615.113673492 -86 4.3 202.628668126 578.814112106 -87 4.32 191.396164684 544.804746089 -88 4.34 180.822239621 512.931545605 -89 4.36 170.865617553 483.051479815 -90 4.38 161.487780703 455.031686127 -91 4.4 152.652773286 428.748705595 -92 4.42 144.327020575 404.087778912 -93 4.44 136.479161479 380.942197972 -94 4.46 129.07989358 359.212708377 -95 4.48 122.101829632 338.806958688 -96 4.5 115.519364658 319.638992577 -97 4.52 109.308552789 301.628780369 -98 4.54 103.446993117 284.701786758 -99 4.56 97.9137238447 268.788571763 -100 4.58 92.6891241175 253.824422244 -101 4.6 87.7548229339 239.749011508 -102 4.62 83.0936146036 226.506084761 -103 4.64 78.6893802546 214.043168343 -104 4.66 74.5270149351 202.31130085 -105 4.68 70.5923598871 191.264784422 -106 4.7 66.8721396072 180.860954593 -107 4.72 63.353903336 171.05996726 -108 4.74 60.0259706488 161.824601429 -109 4.76 56.8773808439 153.120076496 -110 4.78 53.8978458491 144.913882966 -111 4.8 51.0777063884 137.175625538 -112 4.82 48.4078911713 129.876877635 -113 4.84 45.8798788842 122.991046476 -114 4.86 43.485662782 116.493247913 -115 4.88 41.2177176913 110.360190267 -116 4.9 39.0689692529 104.570066494 -117 4.92 37.0327652428 99.1024540566 -118 4.94 35.102848823 93.9382219092 -119 4.96 33.2733335874 89.05944408 -120 4.98 31.5386802724 84.4493193479 -121 5.0 29.8936750183 80.0920965658 -122 5.02 28.3334090704 75.9730052143 -123 5.04 26.8532598202 72.0781907976 -124 5.06 25.4488730938 68.3946547294 -125 5.08 24.116146599 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22.38 -0.00235574158704 -0.0197892047262 -991 22.4 -0.00196048737759 -0.0197362477497 -992 22.42 -0.00156629041861 -0.0196834795391 -993 22.44 -0.00117314694319 -0.0196308992543 -994 22.46 -0.000781053201174 -0.0195785060596 -995 22.48 -0.000390005459079 -0.019526299124 -996 22.5 0.0 -0.0194742776206 -997 22.52 0.0 0.0 -998 22.54 0.0 0.0 -999 22.56 0.0 0.0 -1000 22.58 0.0 0.0 -1001 22.6 0.0 0.0 diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/calc_table.py b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/calc_table.py deleted file mode 100755 index 48f199074c..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/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 = 2.6 -Rmax = 22.6 -Rc1 = 22.0 -Rc2 = 22.5 -N = 1001 - -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_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat deleted file mode 100644 index d7a16e9bc3..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/moltemplate_files/version_charmm_cutoff/table_int.dat +++ /dev/null @@ -1,1020 +0,0 @@ -# Computed with "calc_table.py" -# 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) -# where here sigma = 7.5, and epsilon = 2.75/4.184 -# The interaction is truncated. See below. -# -# In this version I used the CHARMM switching function -# S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3 -# with rc1=22.0 and rc2=22.5 -# 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 also probably with the later Watson JCP 2011 paper. -# (So don't use this.) - -INT -N 1001 R - -1 2.6 87251.787856 402763.664479 -2 2.62 79585.2363621 364574.203947 -3 2.64 72643.024379 330255.845328 -4 2.66 66351.9883051 299391.208536 -5 2.68 60646.8253431 271610.570248 -6 2.7 55469.1990684 246586.123584 -7 2.72 50766.9523602 224026.964698 -8 2.74 46493.4141489 203674.709811 -9 2.76 42606.7882202 185299.659567 -10 2.78 39069.6138645 168697.439095 -11 2.8 35848.2894913 153686.051901 -12 2.82 32912.6514783 140103.294183 -13 2.84 30235.6015217 127804.483324 -14 2.86 27792.7766117 116660.460548 -15 2.88 25562.2565081 106555.833042 -16 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-0.0111676702695 -996 22.5 -0.0 -0.0 -997 22.52 -0.0 -0.0 -998 22.54 -0.0 -0.0 -999 22.56 -0.0 -0.0 -1000 22.58 -0.0 -0.0 -1001 22.6 -0.0 -0.0 diff --git a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.min b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.min deleted file mode 100644 index aaf17a4563..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.min +++ /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_membrane_examples/membrane_BranniganPRE2005/run.in.npt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.npt deleted file mode 100644 index b309e3fb88..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.npt +++ /dev/null @@ -1,56 +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 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 - -# 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_membrane_examples/membrane_BranniganPRE2005/run.in.nvt b/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.nvt deleted file mode 100644 index 54c14b7ce6..0000000000 --- a/tools/moltemplate/examples/CG_membrane_examples/membrane_BranniganPRE2005/run.in.nvt +++ /dev/null @@ -1,40 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -# read_data system.data #<-- commenting out -# Use the pressure-equilibrated restart file instead: -read_restart system_after_npt.rst - - -# -- 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_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 4dd3eea8fc..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_run.sh +++ /dev/null @@ -1,22 +0,0 @@ -# This is just an example. -# -# Note: The files "run.in.min", and "run.in.nvt" are LAMMPS input scripts which -# refer to the input scripts and data files you created earlier: -# 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_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_visualise.txt b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualise.txt deleted file mode 100644 index 5d97ea56ad..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/README_visualise.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.min b/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/run.in.min deleted file mode 100644 index 351da8231e..0000000000 --- a/tools/moltemplate/examples/CG_misc/2bead_heteropolymer/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 2500 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_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 e8e13dec72..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_run.sh +++ /dev/null @@ -1,19 +0,0 @@ -# This is just an example. -# -# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read -# the input scripts and data files you created with 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.nvt - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -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_visualise.txt b/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/README_visualise.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 9ebf85461c..0000000000 --- a/tools/moltemplate/examples/CG_misc/random_heteropolymer/moltemplate_files/monomers.lt +++ /dev/null @@ -1,123 +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 - - - - - # bond-type k r0 - - write_once("Data Bond Coeffs") { - @bond:sidechain 20.0 3.4 - @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. - - # angle-type k theta0 - - write_once("Data Angle Coeffs") { - @angle:backbone 10.00 160 - @angle:sidechain 10.00 120 - @angle:RCR 10.00 120 - } - - # dihedral-type K1 K2 K3 K4 - - write_once("Data Dihedral Coeffs") { - @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 e8e13dec72..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README_run.sh +++ /dev/null @@ -1,19 +0,0 @@ -# This is just an example. -# -# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read -# the input scripts and data files you created with 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.nvt - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt 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_visualise.txt b/tools/moltemplate/examples/CG_misc/translocation/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/README_visualise.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 74e373532c..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 - - 1 !NTITLE - REMARKS VMD generated structure x-plor psf file - - 1716 !NATOM - 1 1 1 1 0.000000 10.0000 0 - 2 2 1 1 0.000000 10.0000 0 - 3 3 1 1 0.000000 10.0000 0 - 4 4 1 1 0.000000 10.0000 0 - 5 5 1 1 0.000000 10.0000 0 - 6 6 1 1 0.000000 10.0000 0 - 7 7 1 1 0.000000 10.0000 0 - 8 8 1 1 0.000000 10.0000 0 - 9 9 1 1 0.000000 10.0000 0 - 10 10 1 1 0.000000 10.0000 0 - 11 11 1 1 0.000000 10.0000 0 - 12 12 1 1 0.000000 10.0000 0 - 13 13 1 1 0.000000 10.0000 0 - 14 14 1 1 0.000000 10.0000 0 - 15 15 1 1 0.000000 10.0000 0 - 16 16 1 1 0.000000 10.0000 0 - 17 17 1 1 0.000000 10.0000 0 - 18 18 1 1 0.000000 10.0000 0 - 19 19 1 1 0.000000 10.0000 0 - 20 20 1 1 0.000000 10.0000 0 - 21 21 1 1 0.000000 10.0000 0 - 22 22 1 1 0.000000 10.0000 0 - 23 23 1 1 0.000000 10.0000 0 - 24 24 1 1 0.000000 10.0000 0 - 25 25 1 1 0.000000 10.0000 0 - 26 26 1 1 0.000000 10.0000 0 - 27 27 1 1 0.000000 10.0000 0 - 28 28 1 1 0.000000 10.0000 0 - 29 29 1 1 0.000000 10.0000 0 - 30 30 1 1 0.000000 10.0000 0 - 31 31 1 1 0.000000 10.0000 0 - 32 32 1 1 0.000000 10.0000 0 - 33 33 1 1 0.000000 10.0000 0 - 34 34 1 1 0.000000 10.0000 0 - 35 35 1 1 0.000000 10.0000 0 - 36 36 1 1 0.000000 10.0000 0 - 37 37 1 1 0.000000 10.0000 0 - 38 38 1 1 0.000000 10.0000 0 - 39 39 1 1 0.000000 10.0000 0 - 40 40 1 1 0.000000 10.0000 0 - 41 41 1 1 0.000000 10.0000 0 - 42 42 1 1 0.000000 10.0000 0 - 43 43 1 1 0.000000 10.0000 0 - 44 44 1 1 0.000000 10.0000 0 - 45 45 1 1 0.000000 10.0000 0 - 46 46 1 1 0.000000 10.0000 0 - 47 47 1 1 0.000000 10.0000 0 - 48 48 1 1 0.000000 10.0000 0 - 49 49 1 1 0.000000 10.0000 0 - 50 50 1 1 0.000000 10.0000 0 - 51 51 1 1 0.000000 10.0000 0 - 52 52 1 1 0.000000 10.0000 0 - 53 53 1 1 0.000000 10.0000 0 - 54 54 1 1 0.000000 10.0000 0 - 55 55 1 1 0.000000 10.0000 0 - 56 56 1 1 0.000000 10.0000 0 - 57 57 1 1 0.000000 10.0000 0 - 58 58 1 1 0.000000 10.0000 0 - 59 59 1 1 0.000000 10.0000 0 - 60 60 1 1 0.000000 10.0000 0 - 61 61 1 1 0.000000 10.0000 0 - 62 62 1 1 0.000000 10.0000 0 - 63 63 1 1 0.000000 10.0000 0 - 64 64 1 1 0.000000 10.0000 0 - 65 65 1 1 0.000000 10.0000 0 - 66 66 1 1 0.000000 10.0000 0 - 67 67 1 1 0.000000 10.0000 0 - 68 68 1 1 0.000000 10.0000 0 - 69 69 1 1 0.000000 10.0000 0 - 70 70 1 1 0.000000 10.0000 0 - 71 71 1 1 0.000000 10.0000 0 - 72 72 1 1 0.000000 10.0000 0 - 73 73 1 1 0.000000 10.0000 0 - 74 74 1 1 0.000000 10.0000 0 - 75 75 1 1 0.000000 10.0000 0 - 76 76 1 1 0.000000 10.0000 0 - 77 77 1 1 0.000000 10.0000 0 - 78 78 1 1 0.000000 10.0000 0 - 79 79 1 1 0.000000 10.0000 0 - 80 80 1 1 0.000000 10.0000 0 - 81 81 1 1 0.000000 10.0000 0 - 82 82 1 1 0.000000 10.0000 0 - 83 83 1 1 0.000000 10.0000 0 - 84 84 1 1 0.000000 10.0000 0 - 85 85 1 1 0.000000 10.0000 0 - 86 86 1 1 0.000000 10.0000 0 - 87 87 1 1 0.000000 10.0000 0 - 88 88 1 1 0.000000 10.0000 0 - 89 89 1 1 0.000000 10.0000 0 - 90 90 1 1 0.000000 10.0000 0 - 91 91 1 1 0.000000 10.0000 0 - 92 92 1 1 0.000000 10.0000 0 - 93 93 1 1 0.000000 10.0000 0 - 94 94 1 1 0.000000 10.0000 0 - 95 95 1 1 0.000000 10.0000 0 - 96 96 1 1 0.000000 10.0000 0 - 97 97 1 1 0.000000 10.0000 0 - 98 98 1 1 0.000000 10.0000 0 - 99 99 1 1 0.000000 10.0000 0 - 100 100 1 1 0.000000 10.0000 0 - 101 101 1 1 0.000000 10.0000 0 - 102 102 1 1 0.000000 10.0000 0 - 103 103 1 1 0.000000 10.0000 0 - 104 104 1 1 0.000000 10.0000 0 - 105 105 1 1 0.000000 10.0000 0 - 106 106 1 1 0.000000 10.0000 0 - 107 107 1 1 0.000000 10.0000 0 - 108 108 1 1 0.000000 10.0000 0 - 109 109 1 1 0.000000 10.0000 0 - 110 110 1 1 0.000000 10.0000 0 - 111 111 1 1 0.000000 10.0000 0 - 112 112 1 1 0.000000 10.0000 0 - 113 113 1 1 0.000000 10.0000 0 - 114 114 1 1 0.000000 10.0000 0 - 115 115 1 1 0.000000 10.0000 0 - 116 116 1 1 0.000000 10.0000 0 - 117 117 1 1 0.000000 10.0000 0 - 118 118 1 1 0.000000 10.0000 0 - 119 119 1 1 0.000000 10.0000 0 - 120 120 1 1 0.000000 10.0000 0 - 121 121 1 1 0.000000 10.0000 0 - 122 122 1 1 0.000000 10.0000 0 - 123 123 1 1 0.000000 10.0000 0 - 124 124 1 1 0.000000 10.0000 0 - 125 125 1 1 0.000000 10.0000 0 - 126 126 1 1 0.000000 10.0000 0 - 127 127 1 1 0.000000 10.0000 0 - 128 128 1 1 0.000000 10.0000 0 - 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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 - } - - # bond-type k r0 - - write_once("Data Bond Coeffs") { - @bond:sidechain 30.0 1.2 - @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. - - # angle-type k theta0 - - write_once("Data Angle Coeffs") { - @angle:backbone 50.00 160 - @angle:sidechain 50.00 120 - @angle:RCR 50.00 120 - } - - # dihedral-type K1 K2 K3 K4 - - write_once("Data Dihedral Coeffs") { - @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 89b9135ccb..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/moltemplate_files/system.lt +++ /dev/null @@ -1,53 +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 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 bonded interactions. Delete them too. -# 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 16a532e1a8..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/run.in.npt +++ /dev/null @@ -1,61 +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.) - -# This next line is somewhat controversial. Feel free to delete this next line - -fix Ffreezestuff groupB rigid single force * off off off torque * off off off - -#(Neither Trung or Steve Plimpton use fix rigid for immobilizing objects, but -# I noticed that at NPT, it does a better job of maintaining the correct volume) - -# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the -# forces between immobilized atoms. -neigh_modify exclude group groupB groupB - - -# ------------------- NPT ----------------------- - -# 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 - -thermo_style custom step c_tempMobile c_pressMobile temp press vol - -# 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 - -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 966bcd88f3..0000000000 --- a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt +++ /dev/null @@ -1,35 +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 - -fix 1 mobile nvt temp 300.0 300.0 100.0 - -run 200000 - -write_restart system_after_nvt.rst - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/README.TXT deleted file mode 100644 index 31abcd66ef..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README.TXT deleted file mode 100644 index a52f73ff7b..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/README_visualise.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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/misfolded+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/images/unfolded+chaperonin_t=508750tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d70ea9b1f2..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_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_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 0.00102967941688 -42 0.205 -0.0185299503645 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5.735 1538935.10642 -57819017.4811 -1149 5.74 1860314.59485 -71242218.9505 -1150 5.745 2257134.5845 -88139540.3817 -1151 5.75 2749142.49547 -109506722.176 -1152 5.755 3361811.73098 -136653799.897 -1153 5.76 4128170.65016 -171313840.077 -1154 5.765 5091272.07333 -215792744.495 -1155 5.77 6307548.29223 -273176998.31 -1156 5.775 7851398.52158 -347623759.363 -1157 5.78 9821503.74726 -444768835.455 -1158 5.785 12349580.5127 -572304762.479 -1159 5.79 15612604.744 -740806327.342 -1160 5.795 19850012.3018 -964919124.004 -1161 5.8 25388097.1921 -1265085490.72 -1162 5.805 32674911.255 -1670073366.45 -1163 5.81 42330627.3386 -2220716617.13 -1164 5.815 55220893.742 -2975502155.22 -1165 5.82 72564721.5485 -4019002953.22 -1166 5.825 96094798.4335 -5474746758.15 -1167 5.83 128298297.388 -7525081897.32 -1168 5.835 172782757.396 -10442221387.6 -1169 5.84 234838762.891 -14637386017.7 -1170 5.845 322316442.616 -20739670704.4 -1171 5.85 447009526.718 -29724465089.5 -1172 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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.dat b/tools/moltemplate/examples/CG_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_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 -9.69644189231e-08 -21 0.1 8.36392202433e-07 -1.0211811869e-07 -22 0.105 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8.84688718753e-07 -3.42379050225e-07 -66 0.325 8.86415391229e-07 -3.48294435432e-07 -67 0.33 8.88171708466e-07 -3.54237035959e-07 -68 0.335 8.89957807764e-07 -3.60207341438e-07 -69 0.34 8.91773828877e-07 -3.66205844906e-07 -70 0.345 8.93619914037e-07 -3.72233042875e-07 -71 0.35 8.95496207963e-07 -3.78289435392e-07 -72 0.355 8.97402857887e-07 -3.84375526106e-07 -73 0.36 8.99340013567e-07 -3.90491822333e-07 -74 0.365 9.01307827305e-07 -3.96638835124e-07 -75 0.37 9.0330645397e-07 -4.02817079329e-07 -76 0.375 9.05336051015e-07 -4.09027073668e-07 -77 0.38 9.07396778494e-07 -4.152693408e-07 -78 0.385 9.09488799088e-07 -4.21544407387e-07 -79 0.39 9.11612278118e-07 -4.2785280417e-07 -80 0.395 9.13767383571e-07 -4.34195066035e-07 -81 0.4 9.15954286119e-07 -4.40571732086e-07 -82 0.405 9.18173159138e-07 -4.46983345718e-07 -83 0.41 9.20424178735e-07 -4.53430454687e-07 -84 0.415 9.22707523764e-07 -4.59913611186e-07 -85 0.42 9.25023375853e-07 -4.66433371919e-07 -86 0.425 9.27371919425e-07 -4.72990298174e-07 -87 0.43 9.29753341721e-07 -4.795849559e-07 -88 0.435 9.32167832821e-07 -4.86217915785e-07 -89 0.44 9.34615585674e-07 -4.9288975333e-07 -90 0.445 9.37096796117e-07 -4.99601048932e-07 -91 0.45 9.39611662902e-07 -5.0635238796e-07 -92 0.455 9.4216038772e-07 -5.13144360835e-07 -93 0.46 9.44743175226e-07 -5.19977563112e-07 -94 0.465 9.47360233068e-07 -5.26852595561e-07 -95 0.47 9.50011771908e-07 -5.33770064252e-07 -96 0.475 9.52698005456e-07 -5.40730580635e-07 -97 0.48 9.55419150489e-07 -5.47734761627e-07 -98 0.485 9.58175426884e-07 -5.54783229699e-07 -99 0.49 9.60967057644e-07 -5.61876612959e-07 -100 0.495 9.63794268928e-07 -5.69015545241e-07 -101 0.5 9.66657290077e-07 -5.76200666196e-07 -102 0.505 9.69556353647e-07 -5.83432621378e-07 -103 0.51 9.72491695434e-07 -5.90712062337e-07 -104 0.515 9.75463554509e-07 -5.9803964671e-07 -105 0.52 9.78472173246e-07 -6.05416038315e-07 -106 0.525 9.81517797354e-07 -6.12841907243e-07 -107 0.53 9.84600675908e-07 -6.20317929954e-07 -108 0.535 9.87721061381e-07 -6.27844789373e-07 -109 0.54 9.90879209678e-07 -6.3542317499e-07 -110 0.545 9.94075380168e-07 -6.43053782955e-07 -111 0.55 9.97309835716e-07 -6.50737316177e-07 -112 0.555 1.00058284272e-06 -6.58474484431e-07 -113 0.56 1.00389467115e-06 -6.66266004455e-07 -114 0.565 1.00724559456e-06 -6.74112600053e-07 -115 0.57 1.01063589016e-06 -6.82015002204e-07 -116 0.575 1.01406583882e-06 -6.89973949166e-07 -117 0.58 1.01753572513e-06 -6.97990186581e-07 -118 0.585 1.02104583743e-06 -7.06064467589e-07 -119 0.59 1.02459646782e-06 -7.14197552934e-07 -120 0.595 1.02818791224e-06 -7.22390211075e-07 -121 0.6 1.03182047051e-06 -7.30643218304e-07 -122 0.605 1.03549444631e-06 -7.38957358854e-07 -123 0.61 1.0392101473e-06 -7.47333425021e-07 -124 0.615 1.04296788511e-06 -7.55772217275e-07 -125 0.62 1.04676797537e-06 -7.64274544386e-07 -126 0.625 1.0506107378e-06 -7.72841223537e-07 -127 0.63 1.05449649623e-06 -7.81473080451e-07 -128 0.635 1.05842557863e-06 -7.90170949513e-07 -129 0.64 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a/tools/moltemplate/examples/CG_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 -3.78808936748 0.080737451911 -15 14.0 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-359 358.0 -2.41296973939 0.0719124463259 -360 359.0 -2.48521512832 0.072569481568 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.min deleted file mode 100644 index 321ba3c095..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+chaperonin/run.in.nvt deleted file mode 100644 index 7c0855cb8d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README.TXT deleted file mode 100644 index ecb9adad2e..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/README_visualise.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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/images/protein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index e43026ba9f..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/minichaperone.lt deleted file mode 100644 index 1d37823b7a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles deleted file mode 100644 index 7f95d73614..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles +++ /dev/null @@ -1,200 +0,0 @@ -1 1 13 14 15 -2 1 40 41 42 -3 1 67 68 69 -4 1 94 95 96 -5 1 121 122 123 -6 1 148 149 150 -7 1 175 176 177 -8 1 202 203 204 -9 1 7 8 9 -10 1 6 7 8 -11 1 16 17 18 -12 1 34 35 36 -13 1 33 34 35 -14 1 43 44 45 -15 1 61 62 63 -16 1 60 61 62 -17 1 70 71 72 -18 1 88 89 90 -19 1 87 88 89 -20 1 97 98 99 -21 1 115 116 117 -22 1 114 115 116 -23 1 124 125 126 -24 1 142 143 144 -25 1 141 142 143 -26 1 151 152 153 -27 1 169 170 171 -28 1 168 169 170 -29 1 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45 46 47 -149 1 49 50 51 -150 1 48 49 50 -151 1 72 73 74 -152 1 76 77 78 -153 1 75 76 77 -154 1 99 100 101 -155 1 103 104 105 -156 1 102 103 104 -157 1 126 127 128 -158 1 130 131 132 -159 1 129 130 131 -160 1 153 154 155 -161 1 157 158 159 -162 1 156 157 158 -163 1 180 181 182 -164 1 184 185 186 -165 1 183 184 185 -166 1 207 208 209 -167 1 211 212 213 -168 1 210 211 212 -169 1 19 20 21 -170 1 20 21 22 -171 1 23 24 25 -172 1 24 25 26 -173 1 46 47 48 -174 1 47 48 49 -175 1 50 51 52 -176 1 51 52 53 -177 1 73 74 75 -178 1 74 75 76 -179 1 77 78 79 -180 1 78 79 80 -181 1 100 101 102 -182 1 101 102 103 -183 1 104 105 106 -184 1 105 106 107 -185 1 127 128 129 -186 1 128 129 130 -187 1 131 132 133 -188 1 132 133 134 -189 1 154 155 156 -190 1 155 156 157 -191 1 158 159 160 -192 1 159 160 161 -193 1 181 182 183 -194 1 182 183 184 -195 1 185 186 187 -196 1 186 187 188 -197 1 208 209 210 -198 1 209 210 211 -199 1 212 213 214 -200 1 213 214 215 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type deleted file mode 100644 index 6da6450d54..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type +++ /dev/null @@ -1 +0,0 @@ - 1 @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/bond:1beadFrustrated/* @/bond:1beadFrustrated/* diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template deleted file mode 100644 index aa72039fbf..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles By Type.template +++ /dev/null @@ -1 +0,0 @@ - @/angle:1beadFrustrated/backbone @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/atom:1beadFrustrated/* @/bond:1beadFrustrated/* @/bond:1beadFrustrated/* diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template deleted file mode 100644 index 5848e6c2b6..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Angles.template +++ /dev/null @@ -1,200 +0,0 @@ -$/angle:bytype1 @/angle:1beadFrustrated/backbone 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a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms deleted file mode 100644 index 4931bed87d..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Atoms +++ /dev/null @@ -1,224 +0,0 @@ -1 1 2 0.0 17.6 21.7 20.0 -2 1 1 0.0 18.2 21.7 20.8 -3 1 2 0.0 18.8 22.5 20.8 -4 1 1 0.0 19.4 22.5 20.0 -5 1 2 0.0 20.0 21.7 20.0 -6 1 1 0.0 20.6 21.7 20.8 -7 1 3 0.0 21.2 22.5 20.8 -8 1 3 0.0 21.8 22.5 20.0 -9 1 1 0.0 22.4 21.7 20.0 -10 1 2 0.0 23.0 21.7 19.2 -11 1 1 0.0 23.0 20.7 19.2 -12 1 2 0.0 23.0 20.1 20.0 -13 1 1 0.0 23.8 19.5 20.0 -14 1 2 0.0 23.8 18.9 19.2 -15 1 3 0.0 23.0 18.3 19.2 -16 1 3 0.0 23.0 18.3 20.2 -17 1 3 0.0 22.4 17.5 20.2 -18 1 1 0.0 21.8 17.5 19.4 -19 1 1 0.0 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$/dihedral:proteins[1][1][1]/d24 @/dihedral:1beadFrustrated/alpha $/atom:proteins[1][1][1]/a24 $/atom:proteins[1][1][1]/a25 $/atom:proteins[1][1][1]/a26 $/atom:proteins[1][1][1]/a27 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses deleted file mode 100644 index 6d05b1617f..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses +++ /dev/null @@ -1,4 +0,0 @@ - 1 1.0 - 2 1.0 - 3 1.0 - 4 100.0 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template deleted file mode 100644 index b9b23fd560..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/Data Masses.template +++ /dev/null @@ -1,4 +0,0 @@ - @/atom:1beadFrustrated/B 1.0 - @/atom:1beadFrustrated/L 1.0 - @/atom:1beadFrustrated/N 1.0 - @/atom:Minichaperone/C 100.0 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init deleted file mode 100644 index 1a2282f0a1..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init +++ /dev/null @@ -1,21 +0,0 @@ - # --- 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) - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 - 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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template deleted file mode 100644 index 1a2282f0a1..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Init.template +++ /dev/null @@ -1,21 +0,0 @@ - # --- 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) - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 - 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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings deleted file mode 100644 index a3d5ac7c70..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings +++ /dev/null @@ -1,30 +0,0 @@ - pair_coeff 1 1 lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff 1 2 lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff 1 3 lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff 2 2 lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff 2 3 lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff 3 3 lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - bond_coeff 1 harmonic 100.0 1.0 - angle_coeff 1 harmonic 13.3333333333 105.0 - # style file keyword - dihedral_coeff 2 table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff 1 table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - # Optional: define the atoms in the "proteins" group - group proteins type 1 - group proteins type 2 - group proteins type 3 - # 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 4 4 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 4 - pair_coeff 4 1 table table_minichaperone_h=0.6.dat CH_H0.6 - pair_coeff 4 2 table table_minichaperone_h=0.dat CH_H0 - pair_coeff 4 3 table table_minichaperone_h=0.dat CH_H0 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template deleted file mode 100644 index 38a0070ac9..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/In Settings.template +++ /dev/null @@ -1,30 +0,0 @@ - pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/B lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/L lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff @/atom:1beadFrustrated/B @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff @/atom:1beadFrustrated/L @/atom:1beadFrustrated/L lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff @/atom:1beadFrustrated/L @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff @/atom:1beadFrustrated/N @/atom:1beadFrustrated/N lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - bond_coeff @/bond:1beadFrustrated/backbone harmonic 100.0 1.0 - angle_coeff @/angle:1beadFrustrated/backbone harmonic 13.3333333333 105.0 - # style file keyword - dihedral_coeff @/dihedral:1beadFrustrated/alpha table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff @/dihedral:1beadFrustrated/beta table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - # Optional: define the atoms in the "proteins" group - group proteins type @/atom:1beadFrustrated/B - group proteins type @/atom:1beadFrustrated/L - group proteins type @/atom:1beadFrustrated/N - # 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:Minichaperone/C @/atom:Minichaperone/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:Minichaperone/C - 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 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt deleted file mode 100644 index e28394ee6b..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/output_ttree/ttree_assignments.txt +++ /dev/null @@ -1,808 +0,0 @@ -@/atom:Minichaperone/C 4 -@/atom:1beadFrustrated/B 1 -@/atom:1beadFrustrated/L 2 -@/atom:1beadFrustrated/N 3 -@/angle:1beadFrustrated/backbone 1 -@/bond:1beadFrustrated/backbone 1 -@/dihedral:1beadFrustrated/alpha 2 -@/dihedral:1beadFrustrated/beta 1 -$/atom:proteins[0][0][0]/a1 1 -$/atom:proteins[0][0][0]/a2 2 -$/atom:proteins[0][0][0]/a3 3 -$/atom:proteins[0][0][0]/a4 4 -$/atom:proteins[0][0][0]/a5 5 -$/atom:proteins[0][0][0]/a6 6 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a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data deleted file mode 100644 index aadace6002..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.data +++ /dev/null @@ -1,820 +0,0 @@ -LAMMPS Description - - 224 atoms - 208 bonds - 200 angles - 152 dihedrals - 0 impropers - - 4 atom types - 1 bond types - 1 angle types - 2 dihedral types - - 0.0 80.0 xlo xhi - 0.0 80.0 ylo yhi - 0.0 80.0 zlo zhi - -Masses - - 1 1.0 - 2 1.0 - 3 1.0 - 4 100.0 - -Atoms - -1 1 2 0.0 17.6 21.7 20.0 -2 1 1 0.0 18.2 21.7 20.8 -3 1 2 0.0 18.8 22.5 20.8 -4 1 1 0.0 19.4 22.5 20.0 -5 1 2 0.0 20.0 21.7 20.0 -6 1 1 0.0 20.6 21.7 20.8 -7 1 3 0.0 21.2 22.5 20.8 -8 1 3 0.0 21.8 22.5 20.0 -9 1 1 0.0 22.4 21.7 20.0 -10 1 2 0.0 23.0 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62.5 60.8 -85 4 1 0.0 19.4 62.5 60.0 -86 4 2 0.0 20.0 61.7 60.0 -87 4 1 0.0 20.6 61.7 60.8 -88 4 3 0.0 21.2 62.5 60.8 -89 4 3 0.0 21.8 62.5 60.0 -90 4 1 0.0 22.4 61.7 60.0 -91 4 2 0.0 23.0 61.7 59.2 -92 4 1 0.0 23.0 60.7 59.2 -93 4 2 0.0 23.0 60.1 60.0 -94 4 1 0.0 23.8 59.5 60.0 -95 4 2 0.0 23.8 58.9 59.2 -96 4 3 0.0 23.0 58.3 59.2 -97 4 3 0.0 23.0 58.3 60.2 -98 4 3 0.0 22.4 57.5 60.2 -99 4 1 0.0 21.8 57.5 59.4 -100 4 1 0.0 21.2 58.3 59.4 -101 4 2 0.0 20.6 58.3 60.2 -102 4 2 0.0 20.0 57.5 60.2 -103 4 1 0.0 19.4 57.5 59.4 -104 4 1 0.0 18.8 58.3 59.4 -105 4 2 0.0 18.2 58.3 60.2 -106 4 2 0.0 17.6 57.5 60.2 -107 4 1 0.0 17.0 57.5 59.4 -108 4 2 0.0 16.4 58.3 59.4 -109 5 2 0.0 57.6 21.7 20.0 -110 5 1 0.0 58.2 21.7 20.8 -111 5 2 0.0 58.8 22.5 20.8 -112 5 1 0.0 59.4 22.5 20.0 -113 5 2 0.0 60.0 21.7 20.0 -114 5 1 0.0 60.6 21.7 20.8 -115 5 3 0.0 61.2 22.5 20.8 -116 5 3 0.0 61.8 22.5 20.0 -117 5 1 0.0 62.4 21.7 20.0 -118 5 2 0.0 63.0 21.7 19.2 -119 5 1 0.0 63.0 20.7 19.2 -120 5 2 0.0 63.0 20.1 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18 19 -138 1 44 45 46 -139 1 71 72 73 -140 1 98 99 100 -141 1 125 126 127 -142 1 152 153 154 -143 1 179 180 181 -144 1 206 207 208 -145 1 18 19 20 -146 1 22 23 24 -147 1 21 22 23 -148 1 45 46 47 -149 1 49 50 51 -150 1 48 49 50 -151 1 72 73 74 -152 1 76 77 78 -153 1 75 76 77 -154 1 99 100 101 -155 1 103 104 105 -156 1 102 103 104 -157 1 126 127 128 -158 1 130 131 132 -159 1 129 130 131 -160 1 153 154 155 -161 1 157 158 159 -162 1 156 157 158 -163 1 180 181 182 -164 1 184 185 186 -165 1 183 184 185 -166 1 207 208 209 -167 1 211 212 213 -168 1 210 211 212 -169 1 19 20 21 -170 1 20 21 22 -171 1 23 24 25 -172 1 24 25 26 -173 1 46 47 48 -174 1 47 48 49 -175 1 50 51 52 -176 1 51 52 53 -177 1 73 74 75 -178 1 74 75 76 -179 1 77 78 79 -180 1 78 79 80 -181 1 100 101 102 -182 1 101 102 103 -183 1 104 105 106 -184 1 105 106 107 -185 1 127 128 129 -186 1 128 129 130 -187 1 131 132 133 -188 1 132 133 134 -189 1 154 155 156 -190 1 155 156 157 -191 1 158 159 160 -192 1 159 160 161 -193 1 181 182 183 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73 -50 2 71 72 73 74 -51 2 72 73 74 75 -52 2 73 74 75 76 -53 2 74 75 76 77 -54 2 75 76 77 78 -55 2 76 77 78 79 -56 2 77 78 79 80 -57 2 78 79 80 81 -58 1 82 83 84 85 -59 1 83 84 85 86 -60 1 84 85 86 87 -61 1 85 86 87 88 -62 1 89 90 91 92 -63 1 90 91 92 93 -64 1 91 92 93 94 -65 1 92 93 94 95 -66 1 93 94 95 96 -67 2 96 97 98 99 -68 2 97 98 99 100 -69 2 98 99 100 101 -70 2 99 100 101 102 -71 2 100 101 102 103 -72 2 101 102 103 104 -73 2 102 103 104 105 -74 2 103 104 105 106 -75 2 104 105 106 107 -76 2 105 106 107 108 -77 1 109 110 111 112 -78 1 110 111 112 113 -79 1 111 112 113 114 -80 1 112 113 114 115 -81 1 116 117 118 119 -82 1 117 118 119 120 -83 1 118 119 120 121 -84 1 119 120 121 122 -85 1 120 121 122 123 -86 2 123 124 125 126 -87 2 124 125 126 127 -88 2 125 126 127 128 -89 2 126 127 128 129 -90 2 127 128 129 130 -91 2 128 129 130 131 -92 2 129 130 131 132 -93 2 130 131 132 133 -94 2 131 132 133 134 -95 2 132 133 134 135 -96 1 136 137 138 139 -97 1 137 138 139 140 -98 1 138 139 140 141 -99 1 139 140 141 142 -100 1 143 144 145 146 -101 1 144 145 146 147 -102 1 145 146 147 148 -103 1 146 147 148 149 -104 1 147 148 149 150 -105 2 150 151 152 153 -106 2 151 152 153 154 -107 2 152 153 154 155 -108 2 153 154 155 156 -109 2 154 155 156 157 -110 2 155 156 157 158 -111 2 156 157 158 159 -112 2 157 158 159 160 -113 2 158 159 160 161 -114 2 159 160 161 162 -115 1 163 164 165 166 -116 1 164 165 166 167 -117 1 165 166 167 168 -118 1 166 167 168 169 -119 1 170 171 172 173 -120 1 171 172 173 174 -121 1 172 173 174 175 -122 1 173 174 175 176 -123 1 174 175 176 177 -124 2 177 178 179 180 -125 2 178 179 180 181 -126 2 179 180 181 182 -127 2 180 181 182 183 -128 2 181 182 183 184 -129 2 182 183 184 185 -130 2 183 184 185 186 -131 2 184 185 186 187 -132 2 185 186 187 188 -133 2 186 187 188 189 -134 1 190 191 192 193 -135 1 191 192 193 194 -136 1 192 193 194 195 -137 1 193 194 195 196 -138 1 197 198 199 200 -139 1 198 199 200 201 -140 1 199 200 201 202 -141 1 200 201 202 203 -142 1 201 202 203 204 -143 2 204 205 206 207 -144 2 205 206 207 208 -145 2 206 207 208 209 -146 2 207 208 209 210 -147 2 208 209 210 211 -148 2 209 210 211 212 -149 2 210 211 212 213 -150 2 211 212 213 214 -151 2 212 213 214 215 -152 2 213 214 215 216 - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in deleted file mode 100644 index 3bc8ede7b5..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in +++ /dev/null @@ -1,41 +0,0 @@ - - -# ----------------- Init Section ----------------- - -include "system.in.init" - - -# ----------------- Atom Definition Section ----------------- - -read_data "system.data" - -# ----------------- Settings Section ----------------- - -include "system.in.settings" - - -# ----------------- Run Section ----------------- - -# The lines above define the system you want to simulate. -# What you do next is up to you. -# Typically a user would minimize and equilibrate -# the system using commands similar to the following: -# ---- examples ---- -# -# -- minimize -- -# minimize 1.0e-5 1.0e-7 1000 10000 -# (Note: Some fixes, for example "shake", interfere with the minimize command, -# You can use the "unfix" command to disable them before minimization.) -# -- declare time step for normal MD -- -# timestep 1.0 -# -- run at constant pressure (Nose-Hoover)-- -# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -# -- ALTERNATELY, run at constant volume (Nose-Hoover) -- -# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -# -- ALTERNATELY, run at constant volume using Langevin dynamics. -- -# -- (This is good for sparse CG polymers in implicit solvent.) -- -fix fxlan all langevin 300.0 300.0 5000 48279 -# -- Now, finally run the simulation -- -# run 50000 -# ---- (end of examples) ---- - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init deleted file mode 100644 index 1a2282f0a1..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.init +++ /dev/null @@ -1,21 +0,0 @@ - # --- 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) - units lj - atom_style full - pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 8.0 9.0 - 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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings deleted file mode 100644 index aaa365fa57..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.in.settings +++ /dev/null @@ -1,30 +0,0 @@ - pair_coeff 1 1 lj/charmm/coul/charmm/inter 1.0 1.0 1 -1 - pair_coeff 1 2 lj/charmm/coul/charmm/inter 0.5833333333 1.0 1 0 - pair_coeff 1 3 lj/charmm/coul/charmm/inter 0.6666666667 1.0 1 0 - pair_coeff 2 2 lj/charmm/coul/charmm/inter 0.1666666667 1.0 1 1 - pair_coeff 2 3 lj/charmm/coul/charmm/inter 0.25 1.0 1 0 - pair_coeff 3 3 lj/charmm/coul/charmm/inter 0.3333333333 1.0 1 0 - bond_coeff 1 harmonic 100.0 1.0 - angle_coeff 1 harmonic 13.3333333333 105.0 - # style file keyword - dihedral_coeff 2 table table_dihedral_frustrated.dat FRUSTRATED_ALPHA - dihedral_coeff 1 table table_dihedral_frustrated.dat FRUSTRATED_BETA - # No need to specify dihedral interactions in the turn regions. (none exist) - # Optional: define the atoms in the "proteins" group - group proteins type 1 - group proteins type 2 - group proteins type 3 - # 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 4 4 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 4 -pair_coeff 1 4 table table_minichaperone_h=0.6.dat CH_H0.6 -pair_coeff 2 4 table table_minichaperone_h=0.dat CH_H0 -pair_coeff 3 4 table table_minichaperone_h=0.dat CH_H0 diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/system.lt deleted file mode 100644 index 8f8c37d08b..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_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_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 0.0782867227197 -20 19.0 -4.26439612115 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-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 -3.00537575069 0.0755567150326 -8 7.0 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a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.6.dat b/tools/moltemplate/examples/CG_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_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 3.395 23881.9094124 613718.268337 -61 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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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/moltemplate_files/table_minichaperone_h=0.dat b/tools/moltemplate/examples/CG_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_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 389.095496464 -135 3.77 27.296848588 361.745071901 -136 3.775 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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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.min deleted file mode 100644 index e2d4a5cce4..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated+minichaperone/run.in.nvt deleted file mode 100644 index 523a16575a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README.TXT deleted file mode 100644 index 77af3de15a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_run.sh deleted file mode 100755 index 99338c7708..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/README_visualise.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_protein_folding_examples/1bead+chaperone/frustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg b/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/images/initial_conformation_t=0tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg b/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/images/misfolded_conformation_t=1250tau.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated.lt deleted file mode 100644 index 074b55c735..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/1beadFrustrated_variants.lt deleted file mode 100644 index 54e2de4376..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/generate_tables/calc_dihedral_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/system.lt deleted file mode 100644 index a27595559e..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/moltemplate_files/table_dihedral_frustrated.dat deleted file mode 100644 index d660fee308..0000000000 --- a/tools/moltemplate/examples/CG_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 -4.49328703609 0.0749161804868 -24 23.0 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a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/frustrated/run_short_sim.in.nvt deleted file mode 100644 index 2974c12e8a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README.TXT deleted file mode 100644 index 5da41b9a8b..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_setup.sh deleted file mode 100755 index f2462426f1..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/README_visualise.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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/images/unfrustrated+chaperonin_t=105tau_LR.jpg b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/chaperonin.lt deleted file mode 100644 index 8266d2a898..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/generate_tables/calc_chaperone_table.py b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/system.lt deleted file mode 100644 index d8781c26f5..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/moltemplate_files/table_chaperonin_h=0.475.dat b/tools/moltemplate/examples/CG_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_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 0.045 -0.0184272698161 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b/tools/moltemplate/examples/CG_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_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 -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 -9.69644189231e-08 -21 0.1 8.36392202433e-07 -1.0211811869e-07 -22 0.105 8.36915693374e-07 -1.07279584798e-07 -23 0.11 8.37465011883e-07 -1.12449212192e-07 -24 0.115 8.38040199757e-07 -1.17627396792e-07 -25 0.12 8.38641300774e-07 -1.22814535539e-07 -26 0.125 8.392683607e-07 -1.28011026445e-07 -27 0.13 8.39921427291e-07 -1.33217268641e-07 -28 0.135 8.40600550305e-07 -1.38433662423e-07 -29 0.14 8.41305781504e-07 -1.43660609303e-07 -30 0.145 8.42037174658e-07 -1.48898512057e-07 -31 0.15 8.42794785557e-07 -1.54147774771e-07 -32 0.155 8.43578672015e-07 -1.59408802894e-07 -33 0.16 8.44388893873e-07 -1.64682003285e-07 -34 0.165 8.45225513015e-07 -1.69967784262e-07 -35 0.17 8.46088593367e-07 -1.75266555654e-07 -36 0.175 8.46978200908e-07 -1.80578728847e-07 -37 0.18 8.4789440368e-07 -1.85904716839e-07 -38 0.185 8.48837271792e-07 -1.91244934288e-07 -39 0.19 8.49806877432e-07 -1.96599797561e-07 -40 0.195 8.50803294874e-07 -2.01969724788e-07 -41 0.2 8.51826600486e-07 -2.07355135913e-07 -42 0.205 8.52876872743e-07 -2.12756452745e-07 -43 0.21 8.5395419223e-07 -2.18174099007e-07 -44 0.215 8.55058641658e-07 -2.23608500394e-07 -45 0.22 8.56190305871e-07 -2.29060084623e-07 -46 0.225 8.57349271858e-07 -2.34529281482e-07 -47 0.23 8.5853562876e-07 -2.40016522891e-07 -48 0.235 8.59749467885e-07 -2.4552224295e-07 -49 0.24 8.60990882715e-07 -2.51046877993e-07 -50 0.245 8.62259968921e-07 -2.56590866647e-07 -51 0.25 8.63556824372e-07 -2.62154649881e-07 -52 0.255 8.64881549149e-07 -2.67738671065e-07 -53 0.26 8.66234245555e-07 -2.73343376025e-07 -54 0.265 8.67615018129e-07 -2.78969213098e-07 -55 0.27 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-2.55154000294e+12 - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated+chaperonin/run.in.nvt deleted file mode 100644 index 5fb8d71b39..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README.TXT deleted file mode 100644 index b2770e3e3d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_setup.sh deleted file mode 100755 index cb3196cf8a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/README_visualise.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_protein_folding_examples/1bead+chaperone/unfrustrated/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg b/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=0tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg b/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/images/unfrustrated_t=200tau_LR.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated.lt deleted file mode 100644 index 0dc1f5dd05..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/1beadUnfrustrated_variants.lt deleted file mode 100644 index cbc8fe217c..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/moltemplate_files/system.lt deleted file mode 100644 index 5ebe6efb88..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1bead+chaperone/unfrustrated/run.in.nvt deleted file mode 100644 index a831a97b4a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1beadProtSci2010/README.TXT b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README.TXT deleted file mode 100644 index 0078be1715..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README.TXT +++ /dev/null @@ -1,44 +0,0 @@ -# -------- REQUIREMENTS: --------- -# 1) This example requires the "CLASS2" package. (Use "make yes-CLASS2") -# 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_protein_folding_examples/1beadProtSci2010/README_run.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_run.sh deleted file mode 100755 index 45bd2d451d..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1beadProtSci2010/README_setup.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_setup.sh deleted file mode 100755 index cb3196cf8a..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1beadProtSci2010/README_visualise.txt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/README_visualise.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_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg deleted file mode 100644 index b4d919f9e6..0000000000 Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4HelixBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg deleted file mode 100644 index cd65146ffa..0000000000 Binary files a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/4SheetBundle_t=0.jpg and /dev/null differ diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/images/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/CG_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_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_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt deleted file mode 100644 index 3ee6ee4e87..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/1beadProtSci2010.lt +++ /dev/null @@ -1,276 +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 class2 - 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 - } - - - - # 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 - - } - - - # 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 - } - - # angleType atomtypes1 2 3 bondtypes1 2 - - write_once("Data Angles By Type") { - @angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:* - } - - - - - - # 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 - } - - - # 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:* * * * - @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 * * * - } - -} # 1beadProtSci2010 (namespace) - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh deleted file mode 100755 index b534e7bf52..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/README.sh +++ /dev/null @@ -1,7 +0,0 @@ -# run moltemplate this way - -moltemplate.sh -overlay-dihdedrals system.lt - -# This will generate various files with names ending in *.in* and *.data -# which are needed by LAMMPS. - diff --git a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt deleted file mode 100644 index fcc6188f71..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010.lt deleted file mode 100644 index a0e305f844..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/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_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.lt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.lt deleted file mode 100644 index dad5ff5483..0000000000 --- a/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/moltemplate_files/versions_with_comments/1beadProtSci2010_charmm.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 2012-8-08, only dihedral_style table or charmm can use this formula. - # (dihedral_style class2 is bugged). - # 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 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_protein_folding_examples/1beadProtSci2010/run.in.min b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/run.in.min deleted file mode 100644 index fce9843aa8..0000000000 --- a/tools/moltemplate/examples/CG_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_protein_folding_examples/1beadProtSci2010/run.in.nvt b/tools/moltemplate/examples/CG_protein_folding_examples/1beadProtSci2010/run.in.nvt deleted file mode 100644 index 925aa2b699..0000000000 --- a/tools/moltemplate/examples/CG_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 250 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 250 #(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_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 9617e16d42..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_run.sh +++ /dev/null @@ -1,25 +0,0 @@ -# This is just an example. -# -# Note: The 3 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files you -# created earlier with moltemplate.sh: -# system.in.init, system.in.settings, system.data, system.in.sw - -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.npt # equilibrate the pressure -#"$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL) - -# 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.npt # equilibrate the pressure -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL) - 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_visualise.txt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/README_visualise.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 - 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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/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/run.in.min b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.min deleted file mode 100644 index 218c1229c3..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/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 500 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_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt deleted file mode 100644 index 936867ef12..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt +++ /dev/null @@ -1,43 +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 -- - -# Here I just read the raw coordinate data generated by moltemplate.sh. -# (If I were more careful, I would minimize the system before the run command.) - -read_data system.data - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 2.0 # <- can be increased to 5.0 or 10.0 if careful -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 535d089b7b..0000000000 --- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt +++ /dev/null @@ -1,43 +0,0 @@ -# -- init section -- -include system.in.init - -# -- atom definition section -- - -# I assume you have already finished these steps: -#read_data system.data -#read_restart system_after_min.rst - -read_restart system_after_npt.rst - - -# -- 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 - - -#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/convert_LAMMPS_to_LT_examples/cnad-cnt/README.TXT b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README.TXT deleted file mode 100644 index 2d94bc36ed..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README.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 "$LAMMPS_BINARY" is the name of the command you use to invoke lammps -(such as lmp_linux, lmp_g++, lmp_mac, lmp_ubuntu, lmp_cygwin, etc...). - ----------- diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh deleted file mode 100755 index d7606aa569..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_lammps.sh +++ /dev/null @@ -1,9 +0,0 @@ - -LAMMPS_BINARY="lmp_ubuntu" # change this if your binary has a different name - -# To verify that the files created by ltemplify.py and moltemplate.sh are -# valid LAMMPS files, you can start a short simulation with them this way: -$LAMMPS_BINARY -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 5b0a31421d..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_ltemplify.sh +++ /dev/null @@ -1,11 +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 - 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 e79e9f40b0..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_run_moltemplate.sh +++ /dev/null @@ -1,16 +0,0 @@ -# After you have used ltemplify to generate the LT files you will need, -# use thhe following command to generate the LAMMPS input script and data file -# (and other auxilliary files) that LAMMPS will need: - -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). - -# 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_visualise.txt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualise.txt deleted file mode 100644 index 3b9be3e9c3..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/README_visualise.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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README.TXT b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README.TXT deleted file mode 100644 index 0e58ef44c7..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_run.sh b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_run.sh deleted file mode 100755 index bf2be9f956..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_run.sh +++ /dev/null @@ -1,31 +0,0 @@ -# You would probably run lammps this way: -# -# lmp_ubuntu -i run.in.nvt - -# The "run.in.nvt" file is a LAMMPS input scripts which refers -# 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 -"$LAMMPS_COMMAND" -i run.in.npt # pressure equilibration -"$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 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_setup.sh deleted file mode 100755 index 5d2be21331..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/README_visualize.txt deleted file mode 100644 index 8063d535f8..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf deleted file mode 100644 index 8ebdc4dc82..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/for_visualization/psf_file_created_by_topotools/system.psf +++ /dev/null @@ -1,1124 +0,0 @@ -PSF - - 1 !NTITLE - REMARKS VMD generated structure x-plor 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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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles deleted file mode 100644 index 689da68448..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles +++ /dev/null @@ -1,260 +0,0 @@ -1 1 2 1 3 -2 1 5 4 6 -3 1 8 7 9 -4 1 11 10 12 -5 1 14 13 15 -6 1 17 16 18 -7 1 20 19 21 -8 1 23 22 24 -9 1 26 25 27 -10 1 29 28 30 -11 1 32 31 33 -12 1 35 34 36 -13 1 38 37 39 -14 1 41 40 42 -15 1 44 43 45 -16 1 47 46 48 -17 1 50 49 51 -18 1 53 52 54 -19 1 56 55 57 -20 1 59 58 60 -21 1 62 61 63 -22 1 65 64 66 -23 1 68 67 69 -24 1 71 70 72 -25 1 74 73 75 -26 1 77 76 78 -27 1 80 79 81 -28 1 83 82 84 -29 1 86 85 87 -30 1 89 88 90 -31 1 92 91 93 -32 1 95 94 96 -33 1 98 97 99 -34 1 101 100 102 -35 1 104 103 105 -36 1 107 106 108 -37 1 110 109 111 -38 1 113 112 114 -39 1 116 115 117 -40 1 119 118 120 -41 1 122 121 123 -42 1 125 124 126 -43 1 128 127 129 -44 1 131 130 132 -45 1 134 133 135 -46 1 137 136 138 -47 1 140 139 141 -48 1 143 142 144 -49 1 146 145 147 -50 1 149 148 150 -51 1 152 151 153 -52 1 155 154 156 -53 1 158 157 159 -54 1 161 160 162 -55 1 164 163 165 -56 1 167 166 168 -57 1 170 169 171 -58 1 173 172 174 -59 1 176 175 177 -60 1 179 178 180 -61 1 182 181 183 -62 1 185 184 186 -63 1 188 187 189 -64 1 191 190 192 -65 1 194 193 195 -66 1 197 196 198 -67 1 200 199 201 -68 1 203 202 204 -69 1 206 205 207 -70 1 209 208 210 -71 1 212 211 213 -72 1 215 214 216 -73 1 218 217 219 -74 1 221 220 222 -75 1 224 223 225 -76 1 227 226 228 -77 1 230 229 231 -78 1 233 232 234 -79 1 236 235 237 -80 1 239 238 240 -81 1 242 241 243 -82 1 245 244 246 -83 1 248 247 249 -84 1 251 250 252 -85 1 254 253 255 -86 1 257 256 258 -87 1 260 259 261 -88 1 263 262 264 -89 1 266 265 267 -90 1 269 268 270 -91 1 272 271 273 -92 1 275 274 276 -93 1 278 277 279 -94 1 281 280 282 -95 1 284 283 285 -96 1 287 286 288 -97 1 290 289 291 -98 1 293 292 294 -99 1 296 295 297 -100 1 299 298 300 -101 1 302 301 303 -102 1 305 304 306 -103 1 308 307 309 -104 1 311 310 312 -105 1 314 313 315 -106 1 317 316 318 -107 1 320 319 321 -108 1 323 322 324 -109 1 326 325 327 -110 1 329 328 330 -111 1 332 331 333 -112 1 335 334 336 -113 1 338 337 339 -114 1 341 340 342 -115 1 344 343 345 -116 1 347 346 348 -117 1 350 349 351 -118 1 353 352 354 -119 1 356 355 357 -120 1 359 358 360 -121 1 362 361 363 -122 1 365 364 366 -123 1 368 367 369 -124 1 371 370 372 -125 1 374 373 375 -126 1 377 376 378 -127 1 380 379 381 -128 1 383 382 384 -129 1 386 385 387 -130 1 389 388 390 -131 1 392 391 393 -132 1 395 394 396 -133 1 398 397 399 -134 1 401 400 402 -135 1 404 403 405 -136 1 407 406 408 -137 1 410 409 411 -138 1 413 412 414 -139 1 416 415 417 -140 1 419 418 420 -141 1 422 421 423 -142 1 425 424 426 -143 1 428 427 429 -144 1 431 430 432 -145 1 434 433 435 -146 1 437 436 438 -147 1 440 439 441 -148 1 443 442 444 -149 1 446 445 447 -150 1 449 448 450 -151 1 452 451 453 -152 1 455 454 456 -153 1 458 457 459 -154 1 461 460 462 -155 1 464 463 465 -156 1 467 466 468 -157 1 470 469 471 -158 1 473 472 474 -159 1 476 475 477 -160 1 479 478 480 -161 1 482 481 483 -162 1 485 484 486 -163 1 488 487 489 -164 1 491 490 492 -165 1 494 493 495 -166 1 497 496 498 -167 1 500 499 501 -168 1 503 502 504 -169 1 506 505 507 -170 1 509 508 510 -171 1 512 511 513 -172 1 515 514 516 -173 1 518 517 519 -174 1 521 520 522 -175 1 524 523 525 -176 1 527 526 528 -177 1 530 529 531 -178 1 533 532 534 -179 1 536 535 537 -180 1 539 538 540 -181 1 542 541 543 -182 1 545 544 546 -183 1 548 547 549 -184 1 551 550 552 -185 1 554 553 555 -186 1 557 556 558 -187 1 560 559 561 -188 1 563 562 564 -189 1 566 565 567 -190 1 569 568 570 -191 1 572 571 573 -192 1 575 574 576 -193 1 578 577 579 -194 1 581 580 582 -195 1 584 583 585 -196 1 587 586 588 -197 1 590 589 591 -198 1 593 592 594 -199 1 596 595 597 -200 1 599 598 600 -201 1 602 601 603 -202 1 605 604 606 -203 1 608 607 609 -204 1 611 610 612 -205 1 614 613 615 -206 1 617 616 618 -207 1 620 619 621 -208 1 623 622 624 -209 1 626 625 627 -210 1 629 628 630 -211 1 632 631 633 -212 1 635 634 636 -213 1 638 637 639 -214 1 641 640 642 -215 1 644 643 645 -216 1 647 646 648 -217 1 650 649 651 -218 1 653 652 654 -219 1 656 655 657 -220 1 659 658 660 -221 1 662 661 663 -222 1 665 664 666 -223 1 668 667 669 -224 1 671 670 672 -225 1 674 673 675 -226 1 677 676 678 -227 1 680 679 681 -228 1 683 682 684 -229 1 686 685 687 -230 1 689 688 690 -231 1 692 691 693 -232 1 695 694 696 -233 1 698 697 699 -234 1 701 700 702 -235 1 704 703 705 -236 1 707 706 708 -237 1 710 709 711 -238 1 713 712 714 -239 1 716 715 717 -240 1 719 718 720 -241 1 722 721 723 -242 1 725 724 726 -243 1 728 727 729 -244 1 731 730 732 -245 1 734 733 735 -246 1 737 736 738 -247 1 740 739 741 -248 1 743 742 744 -249 1 746 745 747 -250 1 749 748 750 -251 1 752 751 753 -252 1 755 754 756 -253 1 758 757 759 -254 1 761 760 762 -255 1 764 763 765 -256 1 767 766 768 -257 1 770 769 771 -258 1 773 772 774 -259 1 776 775 777 -260 1 779 778 780 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles.template b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles.template deleted file mode 100644 index b8fcbdb26d..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Angles.template +++ /dev/null @@ -1,260 +0,0 @@ - $/angle:wat[0]/HOH @/angle:SPCE/HOH $/atom:wat[0]/H1 $/atom:wat[0]/O $/atom:wat[0]/H2 - $/angle:wat[1]/HOH @/angle:SPCE/HOH $/atom:wat[1]/H1 $/atom:wat[1]/O $/atom:wat[1]/H2 - $/angle:wat[2]/HOH @/angle:SPCE/HOH $/atom:wat[2]/H1 $/atom:wat[2]/O $/atom:wat[2]/H2 - $/angle:wat[3]/HOH @/angle:SPCE/HOH $/atom:wat[3]/H1 $/atom:wat[3]/O $/atom:wat[3]/H2 - $/angle:wat[4]/HOH @/angle:SPCE/HOH $/atom:wat[4]/H1 $/atom:wat[4]/O $/atom:wat[4]/H2 - $/angle:wat[5]/HOH @/angle:SPCE/HOH $/atom:wat[5]/H1 $/atom:wat[5]/O $/atom:wat[5]/H2 - $/angle:wat[6]/HOH @/angle:SPCE/HOH $/atom:wat[6]/H1 $/atom:wat[6]/O $/atom:wat[6]/H2 - $/angle:wat[7]/HOH @/angle:SPCE/HOH $/atom:wat[7]/H1 $/atom:wat[7]/O $/atom:wat[7]/H2 - $/angle:wat[8]/HOH @/angle:SPCE/HOH $/atom:wat[8]/H1 $/atom:wat[8]/O $/atom:wat[8]/H2 - $/angle:wat[9]/HOH @/angle:SPCE/HOH $/atom:wat[9]/H1 $/atom:wat[9]/O $/atom:wat[9]/H2 - $/angle:wat[10]/HOH @/angle:SPCE/HOH $/atom:wat[10]/H1 $/atom:wat[10]/O $/atom:wat[10]/H2 - $/angle:wat[11]/HOH @/angle:SPCE/HOH $/atom:wat[11]/H1 $/atom:wat[11]/O $/atom:wat[11]/H2 - $/angle:wat[12]/HOH @/angle:SPCE/HOH $/atom:wat[12]/H1 $/atom:wat[12]/O $/atom:wat[12]/H2 - $/angle:wat[13]/HOH @/angle:SPCE/HOH $/atom:wat[13]/H1 $/atom:wat[13]/O $/atom:wat[13]/H2 - $/angle:wat[14]/HOH @/angle:SPCE/HOH $/atom:wat[14]/H1 $/atom:wat[14]/O $/atom:wat[14]/H2 - $/angle:wat[15]/HOH @/angle:SPCE/HOH $/atom:wat[15]/H1 $/atom:wat[15]/O $/atom:wat[15]/H2 - $/angle:wat[16]/HOH @/angle:SPCE/HOH $/atom:wat[16]/H1 $/atom:wat[16]/O $/atom:wat[16]/H2 - $/angle:wat[17]/HOH @/angle:SPCE/HOH $/atom:wat[17]/H1 $/atom:wat[17]/O $/atom:wat[17]/H2 - $/angle:wat[18]/HOH @/angle:SPCE/HOH $/atom:wat[18]/H1 $/atom:wat[18]/O $/atom:wat[18]/H2 - $/angle:wat[19]/HOH @/angle:SPCE/HOH $/atom:wat[19]/H1 $/atom:wat[19]/O $/atom:wat[19]/H2 - $/angle:wat[20]/HOH @/angle:SPCE/HOH $/atom:wat[20]/H1 $/atom:wat[20]/O $/atom:wat[20]/H2 - $/angle:wat[21]/HOH @/angle:SPCE/HOH $/atom:wat[21]/H1 $/atom:wat[21]/O $/atom:wat[21]/H2 - $/angle:wat[22]/HOH @/angle:SPCE/HOH $/atom:wat[22]/H1 $/atom:wat[22]/O $/atom:wat[22]/H2 - $/angle:wat[23]/HOH @/angle:SPCE/HOH $/atom:wat[23]/H1 $/atom:wat[23]/O $/atom:wat[23]/H2 - $/angle:wat[24]/HOH @/angle:SPCE/HOH $/atom:wat[24]/H1 $/atom:wat[24]/O $/atom:wat[24]/H2 - $/angle:wat[25]/HOH @/angle:SPCE/HOH $/atom:wat[25]/H1 $/atom:wat[25]/O $/atom:wat[25]/H2 - $/angle:wat[26]/HOH @/angle:SPCE/HOH $/atom:wat[26]/H1 $/atom:wat[26]/O $/atom:wat[26]/H2 - $/angle:wat[27]/HOH @/angle:SPCE/HOH $/atom:wat[27]/H1 $/atom:wat[27]/O $/atom:wat[27]/H2 - $/angle:wat[28]/HOH @/angle:SPCE/HOH $/atom:wat[28]/H1 $/atom:wat[28]/O $/atom:wat[28]/H2 - $/angle:wat[29]/HOH @/angle:SPCE/HOH $/atom:wat[29]/H1 $/atom:wat[29]/O $/atom:wat[29]/H2 - $/angle:wat[30]/HOH @/angle:SPCE/HOH $/atom:wat[30]/H1 $/atom:wat[30]/O $/atom:wat[30]/H2 - $/angle:wat[31]/HOH @/angle:SPCE/HOH $/atom:wat[31]/H1 $/atom:wat[31]/O $/atom:wat[31]/H2 - $/angle:wat[32]/HOH @/angle:SPCE/HOH $/atom:wat[32]/H1 $/atom:wat[32]/O $/atom:wat[32]/H2 - $/angle:wat[33]/HOH @/angle:SPCE/HOH $/atom:wat[33]/H1 $/atom:wat[33]/O $/atom:wat[33]/H2 - $/angle:wat[34]/HOH @/angle:SPCE/HOH $/atom:wat[34]/H1 $/atom:wat[34]/O $/atom:wat[34]/H2 - $/angle:wat[35]/HOH @/angle:SPCE/HOH $/atom:wat[35]/H1 $/atom:wat[35]/O $/atom:wat[35]/H2 - $/angle:wat[36]/HOH @/angle:SPCE/HOH $/atom:wat[36]/H1 $/atom:wat[36]/O $/atom:wat[36]/H2 - $/angle:wat[37]/HOH @/angle:SPCE/HOH $/atom:wat[37]/H1 $/atom:wat[37]/O $/atom:wat[37]/H2 - $/angle:wat[38]/HOH @/angle:SPCE/HOH $/atom:wat[38]/H1 $/atom:wat[38]/O $/atom:wat[38]/H2 - $/angle:wat[39]/HOH @/angle:SPCE/HOH $/atom:wat[39]/H1 $/atom:wat[39]/O $/atom:wat[39]/H2 - $/angle:wat[40]/HOH @/angle:SPCE/HOH $/atom:wat[40]/H1 $/atom:wat[40]/O $/atom:wat[40]/H2 - $/angle:wat[41]/HOH @/angle:SPCE/HOH $/atom:wat[41]/H1 $/atom:wat[41]/O $/atom:wat[41]/H2 - $/angle:wat[42]/HOH @/angle:SPCE/HOH $/atom:wat[42]/H1 $/atom:wat[42]/O $/atom:wat[42]/H2 - $/angle:wat[43]/HOH @/angle:SPCE/HOH $/atom:wat[43]/H1 $/atom:wat[43]/O $/atom:wat[43]/H2 - $/angle:wat[44]/HOH @/angle:SPCE/HOH $/atom:wat[44]/H1 $/atom:wat[44]/O $/atom:wat[44]/H2 - $/angle:wat[45]/HOH @/angle:SPCE/HOH $/atom:wat[45]/H1 $/atom:wat[45]/O $/atom:wat[45]/H2 - $/angle:wat[46]/HOH @/angle:SPCE/HOH $/atom:wat[46]/H1 $/atom:wat[46]/O $/atom:wat[46]/H2 - $/angle:wat[47]/HOH @/angle:SPCE/HOH $/atom:wat[47]/H1 $/atom:wat[47]/O $/atom:wat[47]/H2 - $/angle:wat[48]/HOH @/angle:SPCE/HOH $/atom:wat[48]/H1 $/atom:wat[48]/O $/atom:wat[48]/H2 - $/angle:wat[49]/HOH @/angle:SPCE/HOH $/atom:wat[49]/H1 $/atom:wat[49]/O $/atom:wat[49]/H2 - $/angle:wat[50]/HOH @/angle:SPCE/HOH $/atom:wat[50]/H1 $/atom:wat[50]/O $/atom:wat[50]/H2 - $/angle:wat[51]/HOH @/angle:SPCE/HOH $/atom:wat[51]/H1 $/atom:wat[51]/O $/atom:wat[51]/H2 - $/angle:wat[52]/HOH @/angle:SPCE/HOH 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a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms deleted file mode 100644 index f5b03fa560..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms +++ /dev/null @@ -1,780 +0,0 @@ -1 1 1 -0.8476 0.0 0.0 0.0 -2 1 2 0.4238 0.8164904 0.0 0.577359 -3 1 2 0.4238 -0.8164904 0.0 0.577359 -4 2 1 -0.8476 0.0 0.0 0.0 -5 2 2 0.4238 0.8164904 0.0 0.577359 -6 2 2 0.4238 -0.8164904 0.0 0.577359 -7 3 1 -0.8476 0.0 0.0 0.0 -8 3 2 0.4238 0.8164904 0.0 0.577359 -9 3 2 0.4238 -0.8164904 0.0 0.577359 -10 4 1 -0.8476 0.0 0.0 0.0 -11 4 2 0.4238 0.8164904 0.0 0.577359 -12 4 2 0.4238 -0.8164904 0.0 0.577359 -13 5 1 -0.8476 0.0 0.0 0.0 -14 5 2 0.4238 0.8164904 0.0 0.577359 -15 5 2 0.4238 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254 2 0.4238 0.8164904 0.0 0.577359 -762 254 2 0.4238 -0.8164904 0.0 0.577359 -763 255 1 -0.8476 0.0 0.0 0.0 -764 255 2 0.4238 0.8164904 0.0 0.577359 -765 255 2 0.4238 -0.8164904 0.0 0.577359 -766 256 1 -0.8476 0.0 0.0 0.0 -767 256 2 0.4238 0.8164904 0.0 0.577359 -768 256 2 0.4238 -0.8164904 0.0 0.577359 -769 257 1 -0.8476 0.0 0.0 0.0 -770 257 2 0.4238 0.8164904 0.0 0.577359 -771 257 2 0.4238 -0.8164904 0.0 0.577359 -772 258 1 -0.8476 0.0 0.0 0.0 -773 258 2 0.4238 0.8164904 0.0 0.577359 -774 258 2 0.4238 -0.8164904 0.0 0.577359 -775 259 1 -0.8476 0.0 0.0 0.0 -776 259 2 0.4238 0.8164904 0.0 0.577359 -777 259 2 0.4238 -0.8164904 0.0 0.577359 -778 260 1 -0.8476 0.0 0.0 0.0 -779 260 2 0.4238 0.8164904 0.0 0.577359 -780 260 2 0.4238 -0.8164904 0.0 0.577359 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms.template b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms.template deleted file mode 100644 index 4bc0621e98..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Atoms.template +++ /dev/null @@ -1,780 +0,0 @@ -$/atom:wat[0]/O $/mol:wat[0] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[0]/H1 $/mol:wat[0] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[0]/H2 $/mol:wat[0] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[1]/O $/mol:wat[1] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[1]/H1 $/mol:wat[1] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[1]/H2 $/mol:wat[1] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[2]/O $/mol:wat[2] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[2]/H1 $/mol:wat[2] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[2]/H2 $/mol:wat[2] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[3]/O $/mol:wat[3] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[3]/H1 $/mol:wat[3] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[3]/H2 $/mol:wat[3] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[4]/O $/mol:wat[4] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[4]/H1 $/mol:wat[4] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[4]/H2 $/mol:wat[4] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[5]/O $/mol:wat[5] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[5]/H1 $/mol:wat[5] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[5]/H2 $/mol:wat[5] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[6]/O $/mol:wat[6] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[6]/H1 $/mol:wat[6] @/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[6]/H2 $/mol:wat[6] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 -$/atom:wat[7]/O $/mol:wat[7] @/atom:SPCE/O -0.8476 0.0 0.0 0.0 -$/atom:wat[7]/H1 $/mol:wat[7] @/atom:SPCE/H 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@/atom:SPCE/H 0.4238 0.8164904 0.0 0.577359 -$/atom:wat[259]/H2 $/mol:wat[259] @/atom:SPCE/H 0.4238 -0.8164904 0.0 0.577359 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Bonds b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Bonds deleted file mode 100644 index 4f2a139592..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Bonds +++ /dev/null @@ -1,520 +0,0 @@ -1 1 1 2 -2 1 1 3 -3 1 4 5 -4 1 4 6 -5 1 7 8 -6 1 7 9 -7 1 10 11 -8 1 10 12 -9 1 13 14 -10 1 13 15 -11 1 16 17 -12 1 16 18 -13 1 19 20 -14 1 19 21 -15 1 22 23 -16 1 22 24 -17 1 25 26 -18 1 25 27 -19 1 28 29 -20 1 28 30 -21 1 31 32 -22 1 31 33 -23 1 34 35 -24 1 34 36 -25 1 37 38 -26 1 37 39 -27 1 40 41 -28 1 40 42 -29 1 43 44 -30 1 43 45 -31 1 46 47 -32 1 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$/bond:wat[221]/OH2 @/bond:SPCE/OH $/atom:wat[221]/O $/atom:wat[221]/H2 - $/bond:wat[222]/OH1 @/bond:SPCE/OH $/atom:wat[222]/O $/atom:wat[222]/H1 - $/bond:wat[222]/OH2 @/bond:SPCE/OH $/atom:wat[222]/O $/atom:wat[222]/H2 - $/bond:wat[223]/OH1 @/bond:SPCE/OH $/atom:wat[223]/O $/atom:wat[223]/H1 - $/bond:wat[223]/OH2 @/bond:SPCE/OH $/atom:wat[223]/O $/atom:wat[223]/H2 - $/bond:wat[224]/OH1 @/bond:SPCE/OH $/atom:wat[224]/O $/atom:wat[224]/H1 - $/bond:wat[224]/OH2 @/bond:SPCE/OH $/atom:wat[224]/O $/atom:wat[224]/H2 - $/bond:wat[225]/OH1 @/bond:SPCE/OH $/atom:wat[225]/O $/atom:wat[225]/H1 - $/bond:wat[225]/OH2 @/bond:SPCE/OH $/atom:wat[225]/O $/atom:wat[225]/H2 - $/bond:wat[226]/OH1 @/bond:SPCE/OH $/atom:wat[226]/O $/atom:wat[226]/H1 - $/bond:wat[226]/OH2 @/bond:SPCE/OH $/atom:wat[226]/O $/atom:wat[226]/H2 - $/bond:wat[227]/OH1 @/bond:SPCE/OH $/atom:wat[227]/O $/atom:wat[227]/H1 - $/bond:wat[227]/OH2 @/bond:SPCE/OH $/atom:wat[227]/O $/atom:wat[227]/H2 - $/bond:wat[228]/OH1 @/bond:SPCE/OH $/atom:wat[228]/O $/atom:wat[228]/H1 - $/bond:wat[228]/OH2 @/bond:SPCE/OH $/atom:wat[228]/O $/atom:wat[228]/H2 - $/bond:wat[229]/OH1 @/bond:SPCE/OH $/atom:wat[229]/O $/atom:wat[229]/H1 - $/bond:wat[229]/OH2 @/bond:SPCE/OH $/atom:wat[229]/O $/atom:wat[229]/H2 - $/bond:wat[230]/OH1 @/bond:SPCE/OH $/atom:wat[230]/O $/atom:wat[230]/H1 - $/bond:wat[230]/OH2 @/bond:SPCE/OH $/atom:wat[230]/O $/atom:wat[230]/H2 - $/bond:wat[231]/OH1 @/bond:SPCE/OH $/atom:wat[231]/O $/atom:wat[231]/H1 - $/bond:wat[231]/OH2 @/bond:SPCE/OH $/atom:wat[231]/O $/atom:wat[231]/H2 - $/bond:wat[232]/OH1 @/bond:SPCE/OH $/atom:wat[232]/O $/atom:wat[232]/H1 - $/bond:wat[232]/OH2 @/bond:SPCE/OH $/atom:wat[232]/O $/atom:wat[232]/H2 - $/bond:wat[233]/OH1 @/bond:SPCE/OH $/atom:wat[233]/O $/atom:wat[233]/H1 - $/bond:wat[233]/OH2 @/bond:SPCE/OH $/atom:wat[233]/O $/atom:wat[233]/H2 - $/bond:wat[234]/OH1 @/bond:SPCE/OH $/atom:wat[234]/O $/atom:wat[234]/H1 - $/bond:wat[234]/OH2 @/bond:SPCE/OH $/atom:wat[234]/O $/atom:wat[234]/H2 - $/bond:wat[235]/OH1 @/bond:SPCE/OH $/atom:wat[235]/O $/atom:wat[235]/H1 - $/bond:wat[235]/OH2 @/bond:SPCE/OH $/atom:wat[235]/O $/atom:wat[235]/H2 - $/bond:wat[236]/OH1 @/bond:SPCE/OH $/atom:wat[236]/O $/atom:wat[236]/H1 - $/bond:wat[236]/OH2 @/bond:SPCE/OH $/atom:wat[236]/O $/atom:wat[236]/H2 - $/bond:wat[237]/OH1 @/bond:SPCE/OH $/atom:wat[237]/O $/atom:wat[237]/H1 - $/bond:wat[237]/OH2 @/bond:SPCE/OH $/atom:wat[237]/O $/atom:wat[237]/H2 - $/bond:wat[238]/OH1 @/bond:SPCE/OH $/atom:wat[238]/O $/atom:wat[238]/H1 - $/bond:wat[238]/OH2 @/bond:SPCE/OH $/atom:wat[238]/O $/atom:wat[238]/H2 - $/bond:wat[239]/OH1 @/bond:SPCE/OH $/atom:wat[239]/O $/atom:wat[239]/H1 - $/bond:wat[239]/OH2 @/bond:SPCE/OH $/atom:wat[239]/O $/atom:wat[239]/H2 - $/bond:wat[240]/OH1 @/bond:SPCE/OH $/atom:wat[240]/O $/atom:wat[240]/H1 - $/bond:wat[240]/OH2 @/bond:SPCE/OH $/atom:wat[240]/O $/atom:wat[240]/H2 - $/bond:wat[241]/OH1 @/bond:SPCE/OH $/atom:wat[241]/O $/atom:wat[241]/H1 - $/bond:wat[241]/OH2 @/bond:SPCE/OH 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$/bond:wat[248]/OH2 @/bond:SPCE/OH $/atom:wat[248]/O $/atom:wat[248]/H2 - $/bond:wat[249]/OH1 @/bond:SPCE/OH $/atom:wat[249]/O $/atom:wat[249]/H1 - $/bond:wat[249]/OH2 @/bond:SPCE/OH $/atom:wat[249]/O $/atom:wat[249]/H2 - $/bond:wat[250]/OH1 @/bond:SPCE/OH $/atom:wat[250]/O $/atom:wat[250]/H1 - $/bond:wat[250]/OH2 @/bond:SPCE/OH $/atom:wat[250]/O $/atom:wat[250]/H2 - $/bond:wat[251]/OH1 @/bond:SPCE/OH $/atom:wat[251]/O $/atom:wat[251]/H1 - $/bond:wat[251]/OH2 @/bond:SPCE/OH $/atom:wat[251]/O $/atom:wat[251]/H2 - $/bond:wat[252]/OH1 @/bond:SPCE/OH $/atom:wat[252]/O $/atom:wat[252]/H1 - $/bond:wat[252]/OH2 @/bond:SPCE/OH $/atom:wat[252]/O $/atom:wat[252]/H2 - $/bond:wat[253]/OH1 @/bond:SPCE/OH $/atom:wat[253]/O $/atom:wat[253]/H1 - $/bond:wat[253]/OH2 @/bond:SPCE/OH $/atom:wat[253]/O $/atom:wat[253]/H2 - $/bond:wat[254]/OH1 @/bond:SPCE/OH $/atom:wat[254]/O $/atom:wat[254]/H1 - $/bond:wat[254]/OH2 @/bond:SPCE/OH $/atom:wat[254]/O $/atom:wat[254]/H2 - $/bond:wat[255]/OH1 @/bond:SPCE/OH $/atom:wat[255]/O $/atom:wat[255]/H1 - $/bond:wat[255]/OH2 @/bond:SPCE/OH $/atom:wat[255]/O $/atom:wat[255]/H2 - $/bond:wat[256]/OH1 @/bond:SPCE/OH $/atom:wat[256]/O $/atom:wat[256]/H1 - $/bond:wat[256]/OH2 @/bond:SPCE/OH $/atom:wat[256]/O $/atom:wat[256]/H2 - $/bond:wat[257]/OH1 @/bond:SPCE/OH $/atom:wat[257]/O $/atom:wat[257]/H1 - $/bond:wat[257]/OH2 @/bond:SPCE/OH $/atom:wat[257]/O $/atom:wat[257]/H2 - $/bond:wat[258]/OH1 @/bond:SPCE/OH $/atom:wat[258]/O $/atom:wat[258]/H1 - $/bond:wat[258]/OH2 @/bond:SPCE/OH $/atom:wat[258]/O $/atom:wat[258]/H2 - $/bond:wat[259]/OH1 @/bond:SPCE/OH $/atom:wat[259]/O $/atom:wat[259]/H1 - $/bond:wat[259]/OH2 @/bond:SPCE/OH $/atom:wat[259]/O $/atom:wat[259]/H2 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses deleted file mode 100644 index 261e6ea52e..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses +++ /dev/null @@ -1,2 +0,0 @@ - 1 15.9994 - 2 1.008 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses.template b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses.template deleted file mode 100644 index 9558470b87..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/Data Masses.template +++ /dev/null @@ -1,2 +0,0 @@ - @/atom:SPCE/O 15.9994 - @/atom:SPCE/H 1.008 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init deleted file mode 100644 index d01b26e206..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init +++ /dev/null @@ -1,9 +0,0 @@ - # -- 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 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init.template b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init.template deleted file mode 100644 index d01b26e206..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Init.template +++ /dev/null @@ -1,9 +0,0 @@ - # -- 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 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings deleted file mode 100644 index ba1d4626c1..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings +++ /dev/null @@ -1,7 +0,0 @@ - bond_coeff 1 harmonic 200.0 1.0 - angle_coeff 1 harmonic 200.0 109.47 - pair_coeff 1 1 lj/charmm/coul/long 0.1553 3.166 - pair_coeff 2 2 lj/charmm/coul/long 0.0 2.058 - group spce type 1 2 - fix fSHAKE all shake 0.0001 10 100 b 1 a 1 - # (Remember to "unfix" fSHAKE during minimization.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings.template b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings.template deleted file mode 100644 index a30c352147..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/In Settings.template +++ /dev/null @@ -1,7 +0,0 @@ - bond_coeff @/bond:SPCE/OH harmonic 200.0 1.0 - angle_coeff @/angle:SPCE/HOH harmonic 200.0 109.47 - pair_coeff @/atom:SPCE/O @/atom:SPCE/O lj/charmm/coul/long 0.1553 3.166 - pair_coeff @/atom:SPCE/H @/atom:SPCE/H lj/charmm/coul/long 0.0 2.058 - group spce type @/atom:SPCE/O @/atom:SPCE/H - fix fSHAKE all shake 0.0001 10 100 b @/bond:SPCE/OH a @/angle:SPCE/HOH - # (Remember to "unfix" fSHAKE during minimization.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/tmp_atom_coords.dat b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/tmp_atom_coords.dat deleted file mode 100644 index dc8c5f55ce..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/output_ttree/tmp_atom_coords.dat +++ /dev/null @@ -1,780 +0,0 @@ - 3.668 10.082 15.904 - 3.224 10.451 15.101 - 3.092 10.379 16.627 - 6.033 4.876 20.891 - 6.078 5.224 21.798 - 6.592 4.088 20.961 - 5.186 16.696 12.072 - 6.083 16.979 11.816 - 5.337 15.832 12.490 - 8.324 13.811 21.332 - 8.633 13.348 22.112 - 8.506 13.116 20.645 - 3.786 16.318 1.310 - 3.781 15.388 1.196 - 4.528 16.580 0.781 - 6.205 6.991 18.442 - 6.782 7.347 19.152 - 5.309 7.062 18.800 - 2.750 8.844 9.629 - 2.110 8.290 9.998 - 2.164 9.245 8.962 - 3.935 16.195 22.109 - 4.870 16.034 21.985 - 3.655 15.367 22.581 - 10.674 8.909 4.986 - 10.998 8.871 5.932 - 9.748 9.270 5.075 - 0.002 5.667 14.591 - 0.483 5.990 13.830 - 0.608 5.781 15.347 - 9.882 9.156 14.916 - 9.574 9.753 15.597 - 10.021 8.264 15.289 - 1.661 6.681 1.943 - 1.943 5.739 1.981 - 0.778 6.599 1.483 - 4.821 20.603 11.239 - 5.466 20.782 11.963 - 5.384 20.914 10.456 - 15.022 20.855 12.831 - 14.222 20.809 13.292 - 14.673 21.057 11.918 - 1.339 3.782 22.814 - 0.839 3.425 22.087 - 1.775 3.077 23.138 - 0.485 15.137 22.476 - 0.644 15.425 23.349 - 0.312 15.961 21.975 - 10.426 7.604 2.404 - 10.761 8.401 1.994 - 10.248 7.889 3.308 - 4.269 22.752 16.265 - 4.149 23.680 15.888 - 5.061 22.796 16.776 - 10.926 5.365 1.018 - 11.138 4.769 1.754 - 10.657 6.212 1.493 - 8.647 4.314 19.278 - 7.964 3.611 19.326 - 8.043 5.064 19.153 - 8.381 17.319 23.275 - 7.516 17.340 23.695 - 8.431 18.263 23.009 - 4.299 17.774 7.169 - 3.303 17.803 7.322 - 4.533 18.755 6.924 - 8.892 12.977 5.321 - 8.119 12.478 5.443 - 9.342 12.557 4.536 - 2.174 18.468 2.212 - 2.632 17.628 2.203 - 2.931 19.120 2.281 - 13.612 17.680 18.622 - 13.744 17.414 19.508 - 14.526 17.831 18.347 - 9.935 12.876 10.191 - 9.709 12.098 9.634 - 9.472 12.766 11.018 - 7.060 2.074 19.830 - 7.650 1.619 20.528 - 6.148 1.796 20.035 - 13.891 1.919 2.992 - 14.198 2.681 3.422 - 13.212 1.577 3.578 - 8.823 10.581 8.827 - 8.183 10.753 8.148 - 8.389 10.061 9.534 - 9.078 11.967 12.734 - 8.228 11.561 12.993 - 9.512 12.194 13.560 - 10.282 0.640 2.053 - 10.367 0.959 3.016 - 9.743 1.323 1.667 - 4.618 8.125 7.777 - 5.405 7.919 8.314 - 4.002 8.458 8.422 - 3.403 4.687 9.815 - 3.109 5.272 9.097 - 3.817 3.973 9.327 - 3.276 7.465 19.325 - 2.772 6.991 19.964 - 3.604 8.288 19.753 - 3.119 10.325 13.158 - 3.598 10.900 12.512 - 3.440 9.430 12.962 - 2.378 5.806 16.253 - 2.157 6.161 17.099 - 3.301 6.032 16.126 - 6.382 22.271 2.319 - 5.550 22.035 1.847 - 6.859 21.472 2.192 - 4.017 3.905 19.418 - 3.142 4.042 19.132 - 4.582 4.727 19.295 - 2.344 20.472 21.631 - 2.932 20.821 20.945 - 1.467 20.548 21.138 - 14.526 10.532 20.137 - 14.162 9.733 20.503 - 14.466 10.420 19.194 - 5.573 14.804 19.090 - 5.959 15.339 19.808 - 5.869 15.413 18.331 - 5.458 13.097 4.589 - 5.673 13.019 3.612 - 4.899 13.894 4.657 - 4.552 1.370 20.330 - 4.274 2.194 19.953 - 4.235 0.801 19.571 - 5.160 13.744 7.954 - 6.048 13.422 8.207 - 5.008 14.493 8.528 - 10.390 6.386 18.828 - 10.688 6.484 19.731 - 9.844 5.589 18.921 - 1.678 21.942 1.035 - 1.272 21.280 1.592 - 1.498 22.809 1.493 - 9.630 21.547 3.000 - 9.601 22.471 2.643 - 9.287 20.954 2.312 - 2.344 10.571 2.624 - 2.122 10.753 3.553 - 2.947 9.791 2.617 - 0.823 23.668 2.888 - 1.636 23.316 3.340 - 0.253 23.978 3.640 - 2.710 6.185 7.540 - 2.467 6.236 6.561 - 3.410 6.855 7.580 - 6.911 19.458 17.335 - 7.517 20.118 16.957 - 6.315 19.136 16.588 - 13.540 22.220 2.748 - 12.965 22.475 3.462 - 14.428 22.404 3.074 - 10.929 14.750 5.718 - 10.050 14.541 5.408 - 11.401 13.879 5.717 - 0.747 4.469 10.579 - 0.426 3.568 10.339 - 1.505 4.585 9.990 - 5.356 5.388 16.046 - 5.884 6.064 16.461 - 5.592 4.622 16.537 - 10.704 6.721 15.883 - 10.901 6.912 16.836 - 10.127 5.972 15.998 - 11.763 19.614 9.958 - 12.279 20.405 9.866 - 12.435 18.905 9.901 - 7.027 2.224 13.411 - 6.185 2.801 13.535 - 6.692 1.403 13.742 - 4.028 7.699 12.776 - 4.577 7.193 12.138 - 3.171 7.320 12.544 - 12.493 9.451 2.215 - 12.908 9.840 2.987 - 12.982 8.641 2.039 - 11.177 9.610 7.928 - 10.443 10.172 8.053 - 10.866 8.788 8.298 - 1.838 3.206 15.398 - 2.201 4.081 15.545 - 2.117 2.999 14.422 - 1.899 11.624 17.893 - 1.139 11.678 17.305 - 2.258 12.535 17.855 - 9.220 13.904 17.340 - 10.062 14.198 17.738 - 9.394 12.999 17.102 - 3.458 9.868 22.419 - 4.398 10.016 22.654 - 3.448 10.189 21.495 - 15.430 3.274 7.407 - 15.458 2.741 8.157 - 15.933 2.740 6.770 - 13.134 4.535 6.559 - 12.434 3.932 6.938 - 13.959 4.162 6.965 - 10.295 14.066 14.320 - 10.592 14.067 15.226 - 9.322 14.226 14.350 - 7.830 19.751 1.995 - 7.257 19.870 1.247 - 8.329 18.923 1.885 - 15.027 11.249 9.806 - 15.636 10.953 9.104 - 14.929 12.194 9.545 - 10.274 11.448 20.959 - 10.893 11.073 21.654 - 10.344 10.891 20.238 - 11.473 6.075 21.702 - 12.046 5.667 22.431 - 10.554 5.939 22.100 - 6.800 16.659 17.184 - 7.143 16.649 16.327 - 7.109 17.502 17.568 - 14.603 18.110 3.213 - 14.275 17.655 3.963 - 13.842 18.606 2.878 - 4.753 20.139 5.475 - 4.769 21.053 5.846 - 5.663 20.031 5.201 - 1.615 17.355 14.355 - 1.225 16.480 14.420 - 0.859 17.984 14.051 - 11.087 15.787 20.150 - 11.221 14.877 19.698 - 11.936 15.940 20.591 - 9.784 18.060 16.439 - 10.576 18.166 15.922 - 9.941 18.584 17.234 - 2.369 19.620 10.838 - 2.051 19.425 11.701 - 3.347 19.717 10.923 - 15.158 15.218 1.453 - 15.286 16.123 1.160 - 14.175 15.219 1.587 - 7.929 9.601 4.322 - 7.364 10.340 3.912 - 7.318 9.011 4.820 - 11.585 23.121 19.455 - 12.413 23.205 19.982 - 10.816 23.266 20.095 - 3.320 1.439 3.693 - 3.018 1.263 2.795 - 4.218 1.737 3.533 - 8.378 22.836 14.074 - 9.127 23.085 13.478 - 7.806 23.652 14.112 - 4.539 2.605 8.295 - 5.460 2.702 8.123 - 4.434 1.616 8.363 - 8.883 21.581 5.760 - 8.705 22.232 6.446 - 9.357 22.008 5.077 - 12.793 13.364 12.168 - 12.787 13.548 11.223 - 11.995 13.794 12.399 - 6.667 7.547 9.646 - 6.103 6.975 10.296 - 7.558 7.292 10.046 - 0.182 23.403 21.361 - 0.301 23.585 22.346 - 1.001 22.867 21.220 - 11.347 16.007 23.148 - 11.779 15.126 23.087 - 10.586 15.923 22.581 - 10.129 17.485 6.550 - 9.231 17.467 6.920 - 10.108 16.702 5.985 - 4.654 5.717 5.023 - 5.059 5.126 4.395 - 5.409 5.785 5.634 - 12.336 14.905 9.350 - 11.849 15.588 8.883 - 11.568 14.375 9.770 - 5.488 14.255 13.212 - 6.279 14.126 13.709 - 4.864 13.991 13.878 - 3.686 8.353 3.401 - 4.494 7.930 3.084 - 3.041 7.727 3.197 - 15.005 14.526 19.133 - 15.742 13.941 19.238 - 14.746 14.453 18.188 - 15.427 13.899 13.418 - 15.598 14.703 13.915 - 14.569 14.032 12.994 - 15.117 16.342 15.320 - 14.190 16.658 15.235 - 15.725 17.080 14.950 - 13.263 23.513 7.326 - 14.083 23.900 7.689 - 13.669 22.803 6.739 - 10.030 11.441 3.434 - 9.274 10.827 3.422 - 10.533 11.362 2.661 - 10.550 9.544 11.315 - 10.055 10.343 11.396 - 11.460 9.846 11.337 - 2.005 17.796 21.122 - 2.773 17.325 21.598 - 2.173 18.758 21.265 - 13.553 15.240 21.435 - 14.103 14.959 20.726 - 13.422 14.470 21.979 - 11.456 2.350 19.585 - 10.731 2.931 19.730 - 11.546 1.862 20.401 - 13.068 2.914 10.149 - 12.803 2.473 9.295 - 14.010 2.849 10.112 - 5.450 9.067 5.337 - 4.722 8.840 4.711 - 4.939 8.770 6.117 - 3.297 18.771 17.303 - 3.913 19.272 17.825 - 3.616 18.935 16.408 - 6.597 15.954 21.463 - 7.157 15.160 21.200 - 7.205 16.451 22.021 - 1.443 3.980 18.627 - 1.536 3.050 18.247 - 0.589 4.282 18.256 - 3.248 22.876 3.701 - 2.662 22.334 4.248 - 4.106 22.410 3.781 - 8.943 19.607 9.393 - 9.890 19.666 9.174 - 8.551 19.202 8.586 - 7.534 23.313 22.010 - 7.309 22.777 22.738 - 6.697 23.403 21.532 - 13.340 13.560 16.477 - 13.400 13.568 15.542 - 12.852 14.406 16.633 - 8.344 7.845 20.429 - 8.479 8.292 21.236 - 9.102 8.059 19.900 - 6.901 21.557 9.326 - 7.410 20.744 9.384 - 7.474 22.077 8.759 - 14.403 7.815 15.212 - 13.532 8.206 14.911 - 14.885 7.681 14.373 - 6.857 11.138 6.829 - 6.107 11.750 6.800 - 6.480 10.387 6.353 - 10.309 21.500 11.481 - 11.014 20.928 11.185 - 9.595 20.961 11.183 - 13.235 22.943 15.633 - 12.613 22.525 16.194 - 14.027 22.981 16.180 - 6.818 20.066 20.150 - 7.686 20.067 20.626 - 6.969 19.869 19.212 - 7.975 20.030 22.745 - 8.632 20.654 22.435 - 7.441 20.490 23.501 - 12.113 0.921 4.942 - 12.819 0.635 5.562 - 11.814 1.896 5.223 - 9.197 4.375 15.964 - 9.163 3.590 15.387 - 8.516 4.167 16.604 - 2.421 3.775 5.058 - 2.684 2.934 4.652 - 3.219 4.340 5.048 - 6.794 6.875 22.997 - 7.166 7.815 23.093 - 5.834 7.029 23.036 - 11.518 2.141 14.835 - 11.356 2.769 14.101 - 12.345 1.727 14.583 - 3.174 1.584 16.976 - 2.370 2.077 16.810 - 3.270 0.961 16.252 - 10.848 10.071 18.631 - 10.345 10.477 17.907 - 11.663 10.551 18.638 - 12.069 8.766 23.082 - 12.023 9.290 23.888 - 11.590 7.956 23.400 - 5.141 1.611 0.499 - 4.697 1.110 1.234 - 6.031 1.302 0.586 - 2.509 3.505 12.910 - 2.114 4.138 12.315 - 2.715 2.712 12.383 - 14.354 1.352 14.004 - 14.694 0.623 14.565 - 14.573 2.195 14.426 - 14.578 23.489 17.850 - 15.476 23.267 17.861 - 14.359 23.484 18.771 - 5.461 6.754 1.943 - 6.412 6.627 2.018 - 5.209 5.956 1.434 - 14.101 1.902 22.316 - 14.886 2.398 22.002 - 14.108 1.041 21.813 - 6.142 11.858 16.052 - 5.762 12.642 15.675 - 5.566 11.146 15.661 - 11.187 19.104 18.681 - 12.029 18.566 18.863 - 10.574 18.773 19.364 - 11.780 13.509 0.983 - 12.311 13.422 1.794 - 12.379 13.816 0.300 - 13.410 13.796 3.206 - 12.860 13.342 3.952 - 14.378 13.624 3.486 - 7.314 0.228 9.152 - 7.447 0.196 8.157 - 8.219 0.336 9.426 - 0.289 10.538 13.468 - 0.286 10.937 12.602 - 1.262 10.357 13.669 - 12.440 12.407 5.370 - 11.652 11.887 5.105 - 12.893 11.867 5.977 - 6.968 11.629 2.353 - 6.575 10.896 1.807 - 7.083 12.290 1.590 - 13.533 10.550 7.160 - 12.608 10.309 7.490 - 14.008 10.940 7.925 - 13.043 18.831 22.933 - 13.439 17.936 22.986 - 12.139 18.764 23.145 - 11.706 15.811 16.829 - 10.892 16.347 16.590 - 12.344 16.466 17.162 - 11.642 19.030 4.866 - 10.752 18.786 5.209 - 11.534 19.147 3.897 - 13.550 21.522 9.565 - 13.279 21.744 8.655 - 13.859 22.419 9.914 - 12.001 20.877 14.108 - 12.060 21.566 14.774 - 11.186 21.104 13.629 - 12.814 17.906 7.383 - 13.379 17.410 6.688 - 11.963 17.994 6.954 - 15.989 19.751 4.862 - 15.952 20.632 4.460 - 15.557 19.210 4.188 - 10.963 1.737 11.790 - 10.319 2.240 11.334 - 11.709 2.167 11.210 - 5.526 8.369 14.858 - 4.950 8.218 14.072 - 4.945 8.919 15.363 - 14.776 4.939 12.443 - 14.636 5.952 12.252 - 13.865 4.712 12.604 - 7.529 4.508 1.396 - 8.313 4.582 0.857 - 6.783 4.511 0.768 - 11.435 0.836 22.059 - 11.858 0.103 21.657 - 12.219 1.281 22.508 - 11.200 4.151 3.471 - 12.053 4.360 3.928 - 10.572 4.426 4.138 - 4.884 4.081 13.713 - 4.970 4.746 14.373 - 3.932 3.975 13.593 - 13.867 4.624 3.954 - 14.067 4.641 4.904 - 14.122 5.494 3.648 - 3.174 11.159 5.954 - 3.904 11.073 5.352 - 3.204 12.104 6.129 - 12.922 2.911 17.412 - 12.421 2.431 18.089 - 12.240 2.996 16.701 - 13.644 7.961 20.946 - 13.183 7.158 20.680 - 13.018 8.315 21.687 - 6.612 3.396 17.042 - 6.138 2.987 17.830 - 6.248 2.883 16.306 - 3.628 15.453 9.684 - 3.604 16.368 9.365 - 3.266 15.478 10.592 - 1.641 18.264 8.136 - 0.755 18.490 8.008 - 1.981 19.003 8.665 - 8.716 0.819 21.571 - 8.359 0.399 22.460 - 9.622 1.046 21.690 - 14.269 10.001 4.369 - 14.973 10.528 4.752 - 13.690 9.859 5.092 - 14.691 13.817 9.050 - 15.162 14.372 8.385 - 13.821 14.250 9.113 - 12.273 5.424 10.404 - 12.384 4.472 10.210 - 13.153 5.714 10.501 - 3.759 13.253 15.143 - 3.552 13.546 16.059 - 2.862 13.321 14.740 - 7.319 14.432 15.015 - 7.633 15.319 14.742 - 7.702 14.303 15.933 - 3.117 11.819 10.070 - 3.490 12.496 9.523 - 3.937 11.583 10.539 - 0.549 16.393 10.366 - 1.292 16.322 11.016 - 0.665 17.283 9.972 - 10.050 5.605 5.758 - 10.155 6.554 5.556 - 10.797 5.389 6.309 - 7.881 3.518 5.700 - 8.550 4.225 5.812 - 7.070 3.834 6.169 - 8.559 3.515 11.535 - 8.435 4.298 12.155 - 7.955 2.899 11.952 - 13.039 10.511 11.777 - 13.825 10.589 11.282 - 12.883 11.473 11.916 - 15.316 3.976 15.033 - 15.353 4.265 14.065 - 14.585 4.533 15.460 - 8.400 5.552 13.557 - 9.070 5.240 14.185 - 7.739 5.945 14.163 - 4.281 21.161 19.066 - 5.157 21.058 19.381 - 4.169 22.110 18.904 - 13.870 7.474 12.187 - 13.209 8.073 12.633 - 14.457 8.029 11.659 - 13.600 17.247 9.998 - 13.256 16.385 10.107 - 13.616 17.337 9.047 - 10.099 18.083 21.099 - 10.453 17.258 20.699 - 9.398 17.746 21.690 - 15.465 7.955 17.814 - 15.150 7.979 16.932 - 14.706 7.563 18.306 - 9.016 4.086 8.814 - 9.377 5.001 8.813 - 8.726 3.741 9.661 - 6.439 5.144 7.455 - 7.310 4.836 7.837 - 6.121 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-$/angle:wat[224]/HOH 225 -$/angle:wat[225]/HOH 226 -$/angle:wat[226]/HOH 227 -$/angle:wat[227]/HOH 228 -$/angle:wat[228]/HOH 229 -$/angle:wat[229]/HOH 230 -$/angle:wat[230]/HOH 231 -$/angle:wat[231]/HOH 232 -$/angle:wat[232]/HOH 233 -$/angle:wat[233]/HOH 234 -$/angle:wat[234]/HOH 235 -$/angle:wat[235]/HOH 236 -$/angle:wat[236]/HOH 237 -$/angle:wat[237]/HOH 238 -$/angle:wat[238]/HOH 239 -$/angle:wat[239]/HOH 240 -$/angle:wat[240]/HOH 241 -$/angle:wat[241]/HOH 242 -$/angle:wat[242]/HOH 243 -$/angle:wat[243]/HOH 244 -$/angle:wat[244]/HOH 245 -$/angle:wat[245]/HOH 246 -$/angle:wat[246]/HOH 247 -$/angle:wat[247]/HOH 248 -$/angle:wat[248]/HOH 249 -$/angle:wat[249]/HOH 250 -$/angle:wat[250]/HOH 251 -$/angle:wat[251]/HOH 252 -$/angle:wat[252]/HOH 253 -$/angle:wat[253]/HOH 254 -$/angle:wat[254]/HOH 255 -$/angle:wat[255]/HOH 256 -$/angle:wat[256]/HOH 257 -$/angle:wat[257]/HOH 258 -$/angle:wat[258]/HOH 259 -$/angle:wat[259]/HOH 260 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/solvate.pdb deleted file mode 100644 index 0ed5103cbb..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/spce.lt deleted file mode 100644 index 7ed9567d45..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_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 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 all 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/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.data b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.data deleted file mode 100644 index 352e09883a..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.data +++ /dev/null @@ -1,1590 +0,0 @@ -LAMMPS Description - - 780 atoms - 520 bonds - 260 angles - 0 dihedrals - 0 impropers - - 2 atom types - 1 bond types - 1 angle types - - 0.0 16.000 xlo xhi - 0.0 24.000 ylo yhi - 0.0 24.000 zlo zhi - -Masses - - 1 15.9994 - 2 1.008 - -Atoms -# (Note: x,y,z coordinates may overlap and can be modified later.) -1 1 1 -0.8476 0.0 0.0 0.0 -2 1 2 0.4238 0.8164904 0.0 0.577359 -3 1 2 0.4238 -0.8164904 0.0 0.577359 -4 2 1 -0.8476 0.0 0.0 0.0 -5 2 2 0.4238 0.8164904 0.0 0.577359 -6 2 2 0.4238 -0.8164904 0.0 0.577359 -7 3 1 -0.8476 0.0 0.0 0.0 -8 3 2 0.4238 0.8164904 0.0 0.577359 -9 3 2 0.4238 -0.8164904 0.0 0.577359 -10 4 1 -0.8476 0.0 0.0 0.0 -11 4 2 0.4238 0.8164904 0.0 0.577359 -12 4 2 0.4238 -0.8164904 0.0 0.577359 -13 5 1 -0.8476 0.0 0.0 0.0 -14 5 2 0.4238 0.8164904 0.0 0.577359 -15 5 2 0.4238 -0.8164904 0.0 0.577359 -16 6 1 -0.8476 0.0 0.0 0.0 -17 6 2 0.4238 0.8164904 0.0 0.577359 -18 6 2 0.4238 -0.8164904 0.0 0.577359 -19 7 1 -0.8476 0.0 0.0 0.0 -20 7 2 0.4238 0.8164904 0.0 0.577359 -21 7 2 0.4238 -0.8164904 0.0 0.577359 -22 8 1 -0.8476 0.0 0.0 0.0 -23 8 2 0.4238 0.8164904 0.0 0.577359 -24 8 2 0.4238 -0.8164904 0.0 0.577359 -25 9 1 -0.8476 0.0 0.0 0.0 -26 9 2 0.4238 0.8164904 0.0 0.577359 -27 9 2 0.4238 -0.8164904 0.0 0.577359 -28 10 1 -0.8476 0.0 0.0 0.0 -29 10 2 0.4238 0.8164904 0.0 0.577359 -30 10 2 0.4238 -0.8164904 0.0 0.577359 -31 11 1 -0.8476 0.0 0.0 0.0 -32 11 2 0.4238 0.8164904 0.0 0.577359 -33 11 2 0.4238 -0.8164904 0.0 0.577359 -34 12 1 -0.8476 0.0 0.0 0.0 -35 12 2 0.4238 0.8164904 0.0 0.577359 -36 12 2 0.4238 -0.8164904 0.0 0.577359 -37 13 1 -0.8476 0.0 0.0 0.0 -38 13 2 0.4238 0.8164904 0.0 0.577359 -39 13 2 0.4238 -0.8164904 0.0 0.577359 -40 14 1 -0.8476 0.0 0.0 0.0 -41 14 2 0.4238 0.8164904 0.0 0.577359 -42 14 2 0.4238 -0.8164904 0.0 0.577359 -43 15 1 -0.8476 0.0 0.0 0.0 -44 15 2 0.4238 0.8164904 0.0 0.577359 -45 15 2 0.4238 -0.8164904 0.0 0.577359 -46 16 1 -0.8476 0.0 0.0 0.0 -47 16 2 0.4238 0.8164904 0.0 0.577359 -48 16 2 0.4238 -0.8164904 0.0 0.577359 -49 17 1 -0.8476 0.0 0.0 0.0 -50 17 2 0.4238 0.8164904 0.0 0.577359 -51 17 2 0.4238 -0.8164904 0.0 0.577359 -52 18 1 -0.8476 0.0 0.0 0.0 -53 18 2 0.4238 0.8164904 0.0 0.577359 -54 18 2 0.4238 -0.8164904 0.0 0.577359 -55 19 1 -0.8476 0.0 0.0 0.0 -56 19 2 0.4238 0.8164904 0.0 0.577359 -57 19 2 0.4238 -0.8164904 0.0 0.577359 -58 20 1 -0.8476 0.0 0.0 0.0 -59 20 2 0.4238 0.8164904 0.0 0.577359 -60 20 2 0.4238 -0.8164904 0.0 0.577359 -61 21 1 -0.8476 0.0 0.0 0.0 -62 21 2 0.4238 0.8164904 0.0 0.577359 -63 21 2 0.4238 -0.8164904 0.0 0.577359 -64 22 1 -0.8476 0.0 0.0 0.0 -65 22 2 0.4238 0.8164904 0.0 0.577359 -66 22 2 0.4238 -0.8164904 0.0 0.577359 -67 23 1 -0.8476 0.0 0.0 0.0 -68 23 2 0.4238 0.8164904 0.0 0.577359 -69 23 2 0.4238 -0.8164904 0.0 0.577359 -70 24 1 -0.8476 0.0 0.0 0.0 -71 24 2 0.4238 0.8164904 0.0 0.577359 -72 24 2 0.4238 -0.8164904 0.0 0.577359 -73 25 1 -0.8476 0.0 0.0 0.0 -74 25 2 0.4238 0.8164904 0.0 0.577359 -75 25 2 0.4238 -0.8164904 0.0 0.577359 -76 26 1 -0.8476 0.0 0.0 0.0 -77 26 2 0.4238 0.8164904 0.0 0.577359 -78 26 2 0.4238 -0.8164904 0.0 0.577359 -79 27 1 -0.8476 0.0 0.0 0.0 -80 27 2 0.4238 0.8164904 0.0 0.577359 -81 27 2 0.4238 -0.8164904 0.0 0.577359 -82 28 1 -0.8476 0.0 0.0 0.0 -83 28 2 0.4238 0.8164904 0.0 0.577359 -84 28 2 0.4238 -0.8164904 0.0 0.577359 -85 29 1 -0.8476 0.0 0.0 0.0 -86 29 2 0.4238 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1 542 541 543 -182 1 545 544 546 -183 1 548 547 549 -184 1 551 550 552 -185 1 554 553 555 -186 1 557 556 558 -187 1 560 559 561 -188 1 563 562 564 -189 1 566 565 567 -190 1 569 568 570 -191 1 572 571 573 -192 1 575 574 576 -193 1 578 577 579 -194 1 581 580 582 -195 1 584 583 585 -196 1 587 586 588 -197 1 590 589 591 -198 1 593 592 594 -199 1 596 595 597 -200 1 599 598 600 -201 1 602 601 603 -202 1 605 604 606 -203 1 608 607 609 -204 1 611 610 612 -205 1 614 613 615 -206 1 617 616 618 -207 1 620 619 621 -208 1 623 622 624 -209 1 626 625 627 -210 1 629 628 630 -211 1 632 631 633 -212 1 635 634 636 -213 1 638 637 639 -214 1 641 640 642 -215 1 644 643 645 -216 1 647 646 648 -217 1 650 649 651 -218 1 653 652 654 -219 1 656 655 657 -220 1 659 658 660 -221 1 662 661 663 -222 1 665 664 666 -223 1 668 667 669 -224 1 671 670 672 -225 1 674 673 675 -226 1 677 676 678 -227 1 680 679 681 -228 1 683 682 684 -229 1 686 685 687 -230 1 689 688 690 -231 1 692 691 693 -232 1 695 694 696 -233 1 698 697 699 -234 1 701 700 702 -235 1 704 703 705 -236 1 707 706 708 -237 1 710 709 711 -238 1 713 712 714 -239 1 716 715 717 -240 1 719 718 720 -241 1 722 721 723 -242 1 725 724 726 -243 1 728 727 729 -244 1 731 730 732 -245 1 734 733 735 -246 1 737 736 738 -247 1 740 739 741 -248 1 743 742 744 -249 1 746 745 747 -250 1 749 748 750 -251 1 752 751 753 -252 1 755 754 756 -253 1 758 757 759 -254 1 761 760 762 -255 1 764 763 765 -256 1 767 766 768 -257 1 770 769 771 -258 1 773 772 774 -259 1 776 775 777 -260 1 779 778 780 - diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in deleted file mode 100644 index ce4c361e69..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in +++ /dev/null @@ -1,45 +0,0 @@ - - -# ----------------- 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 ----------------- - -# The lines above define the system you want to simulate. -# What you do next is up to you. -# Typically a user would minimize and equilibrate -# the system using commands similar to the following: -# ---- examples ---- -# -# -- minimize -- -# minimize 1.0e-5 1.0e-7 1000 10000 -# (Note: Some fixes, for example "shake", interfere with the minimize command, -# You can use the "unfix" command to disable them before minimization.) -# -- declare time step for normal MD -- -# timestep 1.0 -# -- run at constant pressure (Nose-Hoover)-- -# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0 -# -- ALTERNATELY, run at constant volume (Nose-Hoover) -- -# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1 -# -- ALTERNATELY, run at constant volume using Langevin dynamics. -- -# -- (This is good for sparse CG polymers in implicit solvent.) -- -fix fxlan all langevin 300.0 300.0 5000 48279 -# -- Now, finally run the simulation -- -# run 50000 -# ---- (end of examples) ---- - diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.coords b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.coords deleted file mode 100644 index b565680963..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.coords +++ /dev/null @@ -1,780 +0,0 @@ -set atom 1 x 3.668 y 10.082 z 15.904 image 0 0 0 -set atom 2 x 3.224 y 10.451 z 15.101 image 0 0 0 -set atom 3 x 3.092 y 10.379 z 16.627 image 0 0 0 -set atom 4 x 6.033 y 4.876 z 20.891 image 0 0 0 -set atom 5 x 6.078 y 5.224 z 21.798 image 0 0 0 -set atom 6 x 6.592 y 4.088 z 20.961 image 0 0 0 -set atom 7 x 5.186 y 16.696 z 12.072 image 0 0 0 -set atom 8 x 6.083 y 16.979 z 11.816 image 0 0 0 -set atom 9 x 5.337 y 15.832 z 12.490 image 0 0 0 -set atom 10 x 8.324 y 13.811 z 21.332 image 0 0 0 -set atom 11 x 8.633 y 13.348 z 22.112 image 0 0 0 -set atom 12 x 8.506 y 13.116 z 20.645 image 0 0 0 -set atom 13 x 3.786 y 16.318 z 1.310 image 0 0 0 -set atom 14 x 3.781 y 15.388 z 1.196 image 0 0 0 -set atom 15 x 4.528 y 16.580 z 0.781 image 0 0 0 -set atom 16 x 6.205 y 6.991 z 18.442 image 0 0 0 -set atom 17 x 6.782 y 7.347 z 19.152 image 0 0 0 -set atom 18 x 5.309 y 7.062 z 18.800 image 0 0 0 -set atom 19 x 2.750 y 8.844 z 9.629 image 0 0 0 -set atom 20 x 2.110 y 8.290 z 9.998 image 0 0 0 -set atom 21 x 2.164 y 9.245 z 8.962 image 0 0 0 -set atom 22 x 3.935 y 16.195 z 22.109 image 0 0 0 -set atom 23 x 4.870 y 16.034 z 21.985 image 0 0 0 -set atom 24 x 3.655 y 15.367 z 22.581 image 0 0 0 -set atom 25 x 10.674 y 8.909 z 4.986 image 0 0 0 -set atom 26 x 10.998 y 8.871 z 5.932 image 0 0 0 -set atom 27 x 9.748 y 9.270 z 5.075 image 0 0 0 -set atom 28 x 0.002 y 5.667 z 14.591 image 0 0 0 -set atom 29 x 0.483 y 5.990 z 13.830 image 0 0 0 -set atom 30 x 0.608 y 5.781 z 15.347 image 0 0 0 -set atom 31 x 9.882 y 9.156 z 14.916 image 0 0 0 -set atom 32 x 9.574 y 9.753 z 15.597 image 0 0 0 -set atom 33 x 10.021 y 8.264 z 15.289 image 0 0 0 -set atom 34 x 1.661 y 6.681 z 1.943 image 0 0 0 -set atom 35 x 1.943 y 5.739 z 1.981 image 0 0 0 -set atom 36 x 0.778 y 6.599 z 1.483 image 0 0 0 -set atom 37 x 4.821 y 20.603 z 11.239 image 0 0 0 -set atom 38 x 5.466 y 20.782 z 11.963 image 0 0 0 -set atom 39 x 5.384 y 20.914 z 10.456 image 0 0 0 -set atom 40 x 15.022 y 20.855 z 12.831 image 0 0 0 -set atom 41 x 14.222 y 20.809 z 13.292 image 0 0 0 -set atom 42 x 14.673 y 21.057 z 11.918 image 0 0 0 -set atom 43 x 1.339 y 3.782 z 22.814 image 0 0 0 -set atom 44 x 0.839 y 3.425 z 22.087 image 0 0 0 -set atom 45 x 1.775 y 3.077 z 23.138 image 0 0 0 -set atom 46 x 0.485 y 15.137 z 22.476 image 0 0 0 -set atom 47 x 0.644 y 15.425 z 23.349 image 0 0 0 -set atom 48 x 0.312 y 15.961 z 21.975 image 0 0 0 -set atom 49 x 10.426 y 7.604 z 2.404 image 0 0 0 -set atom 50 x 10.761 y 8.401 z 1.994 image 0 0 0 -set atom 51 x 10.248 y 7.889 z 3.308 image 0 0 0 -set atom 52 x 4.269 y 22.752 z 16.265 image 0 0 0 -set atom 53 x 4.149 y 23.680 z 15.888 image 0 0 0 -set atom 54 x 5.061 y 22.796 z 16.776 image 0 0 0 -set atom 55 x 10.926 y 5.365 z 1.018 image 0 0 0 -set atom 56 x 11.138 y 4.769 z 1.754 image 0 0 0 -set atom 57 x 10.657 y 6.212 z 1.493 image 0 0 0 -set atom 58 x 8.647 y 4.314 z 19.278 image 0 0 0 -set atom 59 x 7.964 y 3.611 z 19.326 image 0 0 0 -set atom 60 x 8.043 y 5.064 z 19.153 image 0 0 0 -set atom 61 x 8.381 y 17.319 z 23.275 image 0 0 0 -set atom 62 x 7.516 y 17.340 z 23.695 image 0 0 0 -set atom 63 x 8.431 y 18.263 z 23.009 image 0 0 0 -set atom 64 x 4.299 y 17.774 z 7.169 image 0 0 0 -set atom 65 x 3.303 y 17.803 z 7.322 image 0 0 0 -set atom 66 x 4.533 y 18.755 z 6.924 image 0 0 0 -set atom 67 x 8.892 y 12.977 z 5.321 image 0 0 0 -set atom 68 x 8.119 y 12.478 z 5.443 image 0 0 0 -set atom 69 x 9.342 y 12.557 z 4.536 image 0 0 0 -set atom 70 x 2.174 y 18.468 z 2.212 image 0 0 0 -set atom 71 x 2.632 y 17.628 z 2.203 image 0 0 0 -set atom 72 x 2.931 y 19.120 z 2.281 image 0 0 0 -set atom 73 x 13.612 y 17.680 z 18.622 image 0 0 0 -set atom 74 x 13.744 y 17.414 z 19.508 image 0 0 0 -set atom 75 x 14.526 y 17.831 z 18.347 image 0 0 0 -set atom 76 x 9.935 y 12.876 z 10.191 image 0 0 0 -set atom 77 x 9.709 y 12.098 z 9.634 image 0 0 0 -set atom 78 x 9.472 y 12.766 z 11.018 image 0 0 0 -set atom 79 x 7.060 y 2.074 z 19.830 image 0 0 0 -set atom 80 x 7.650 y 1.619 z 20.528 image 0 0 0 -set atom 81 x 6.148 y 1.796 z 20.035 image 0 0 0 -set atom 82 x 13.891 y 1.919 z 2.992 image 0 0 0 -set atom 83 x 14.198 y 2.681 z 3.422 image 0 0 0 -set atom 84 x 13.212 y 1.577 z 3.578 image 0 0 0 -set atom 85 x 8.823 y 10.581 z 8.827 image 0 0 0 -set atom 86 x 8.183 y 10.753 z 8.148 image 0 0 0 -set atom 87 x 8.389 y 10.061 z 9.534 image 0 0 0 -set atom 88 x 9.078 y 11.967 z 12.734 image 0 0 0 -set atom 89 x 8.228 y 11.561 z 12.993 image 0 0 0 -set atom 90 x 9.512 y 12.194 z 13.560 image 0 0 0 -set atom 91 x 10.282 y 0.640 z 2.053 image 0 0 0 -set atom 92 x 10.367 y 0.959 z 3.016 image 0 0 0 -set atom 93 x 9.743 y 1.323 z 1.667 image 0 0 0 -set atom 94 x 4.618 y 8.125 z 7.777 image 0 0 0 -set atom 95 x 5.405 y 7.919 z 8.314 image 0 0 0 -set atom 96 x 4.002 y 8.458 z 8.422 image 0 0 0 -set atom 97 x 3.403 y 4.687 z 9.815 image 0 0 0 -set atom 98 x 3.109 y 5.272 z 9.097 image 0 0 0 -set atom 99 x 3.817 y 3.973 z 9.327 image 0 0 0 -set atom 100 x 3.276 y 7.465 z 19.325 image 0 0 0 -set atom 101 x 2.772 y 6.991 z 19.964 image 0 0 0 -set atom 102 x 3.604 y 8.288 z 19.753 image 0 0 0 -set atom 103 x 3.119 y 10.325 z 13.158 image 0 0 0 -set atom 104 x 3.598 y 10.900 z 12.512 image 0 0 0 -set atom 105 x 3.440 y 9.430 z 12.962 image 0 0 0 -set atom 106 x 2.378 y 5.806 z 16.253 image 0 0 0 -set atom 107 x 2.157 y 6.161 z 17.099 image 0 0 0 -set atom 108 x 3.301 y 6.032 z 16.126 image 0 0 0 -set atom 109 x 6.382 y 22.271 z 2.319 image 0 0 0 -set atom 110 x 5.550 y 22.035 z 1.847 image 0 0 0 -set atom 111 x 6.859 y 21.472 z 2.192 image 0 0 0 -set atom 112 x 4.017 y 3.905 z 19.418 image 0 0 0 -set atom 113 x 3.142 y 4.042 z 19.132 image 0 0 0 -set atom 114 x 4.582 y 4.727 z 19.295 image 0 0 0 -set atom 115 x 2.344 y 20.472 z 21.631 image 0 0 0 -set atom 116 x 2.932 y 20.821 z 20.945 image 0 0 0 -set atom 117 x 1.467 y 20.548 z 21.138 image 0 0 0 -set atom 118 x 14.526 y 10.532 z 20.137 image 0 0 0 -set atom 119 x 14.162 y 9.733 z 20.503 image 0 0 0 -set atom 120 x 14.466 y 10.420 z 19.194 image 0 0 0 -set atom 121 x 5.573 y 14.804 z 19.090 image 0 0 0 -set atom 122 x 5.959 y 15.339 z 19.808 image 0 0 0 -set atom 123 x 5.869 y 15.413 z 18.331 image 0 0 0 -set atom 124 x 5.458 y 13.097 z 4.589 image 0 0 0 -set atom 125 x 5.673 y 13.019 z 3.612 image 0 0 0 -set atom 126 x 4.899 y 13.894 z 4.657 image 0 0 0 -set atom 127 x 4.552 y 1.370 z 20.330 image 0 0 0 -set atom 128 x 4.274 y 2.194 z 19.953 image 0 0 0 -set atom 129 x 4.235 y 0.801 z 19.571 image 0 0 0 -set atom 130 x 5.160 y 13.744 z 7.954 image 0 0 0 -set atom 131 x 6.048 y 13.422 z 8.207 image 0 0 0 -set atom 132 x 5.008 y 14.493 z 8.528 image 0 0 0 -set atom 133 x 10.390 y 6.386 z 18.828 image 0 0 0 -set atom 134 x 10.688 y 6.484 z 19.731 image 0 0 0 -set atom 135 x 9.844 y 5.589 z 18.921 image 0 0 0 -set atom 136 x 1.678 y 21.942 z 1.035 image 0 0 0 -set atom 137 x 1.272 y 21.280 z 1.592 image 0 0 0 -set atom 138 x 1.498 y 22.809 z 1.493 image 0 0 0 -set atom 139 x 9.630 y 21.547 z 3.000 image 0 0 0 -set atom 140 x 9.601 y 22.471 z 2.643 image 0 0 0 -set atom 141 x 9.287 y 20.954 z 2.312 image 0 0 0 -set atom 142 x 2.344 y 10.571 z 2.624 image 0 0 0 -set atom 143 x 2.122 y 10.753 z 3.553 image 0 0 0 -set atom 144 x 2.947 y 9.791 z 2.617 image 0 0 0 -set atom 145 x 0.823 y 23.668 z 2.888 image 0 0 0 -set atom 146 x 1.636 y 23.316 z 3.340 image 0 0 0 -set atom 147 x 0.253 y 23.978 z 3.640 image 0 0 0 -set atom 148 x 2.710 y 6.185 z 7.540 image 0 0 0 -set atom 149 x 2.467 y 6.236 z 6.561 image 0 0 0 -set atom 150 x 3.410 y 6.855 z 7.580 image 0 0 0 -set atom 151 x 6.911 y 19.458 z 17.335 image 0 0 0 -set atom 152 x 7.517 y 20.118 z 16.957 image 0 0 0 -set atom 153 x 6.315 y 19.136 z 16.588 image 0 0 0 -set atom 154 x 13.540 y 22.220 z 2.748 image 0 0 0 -set atom 155 x 12.965 y 22.475 z 3.462 image 0 0 0 -set atom 156 x 14.428 y 22.404 z 3.074 image 0 0 0 -set atom 157 x 10.929 y 14.750 z 5.718 image 0 0 0 -set atom 158 x 10.050 y 14.541 z 5.408 image 0 0 0 -set atom 159 x 11.401 y 13.879 z 5.717 image 0 0 0 -set atom 160 x 0.747 y 4.469 z 10.579 image 0 0 0 -set atom 161 x 0.426 y 3.568 z 10.339 image 0 0 0 -set atom 162 x 1.505 y 4.585 z 9.990 image 0 0 0 -set atom 163 x 5.356 y 5.388 z 16.046 image 0 0 0 -set atom 164 x 5.884 y 6.064 z 16.461 image 0 0 0 -set atom 165 x 5.592 y 4.622 z 16.537 image 0 0 0 -set atom 166 x 10.704 y 6.721 z 15.883 image 0 0 0 -set atom 167 x 10.901 y 6.912 z 16.836 image 0 0 0 -set atom 168 x 10.127 y 5.972 z 15.998 image 0 0 0 -set atom 169 x 11.763 y 19.614 z 9.958 image 0 0 0 -set atom 170 x 12.279 y 20.405 z 9.866 image 0 0 0 -set atom 171 x 12.435 y 18.905 z 9.901 image 0 0 0 -set atom 172 x 7.027 y 2.224 z 13.411 image 0 0 0 -set atom 173 x 6.185 y 2.801 z 13.535 image 0 0 0 -set atom 174 x 6.692 y 1.403 z 13.742 image 0 0 0 -set atom 175 x 4.028 y 7.699 z 12.776 image 0 0 0 -set atom 176 x 4.577 y 7.193 z 12.138 image 0 0 0 -set atom 177 x 3.171 y 7.320 z 12.544 image 0 0 0 -set atom 178 x 12.493 y 9.451 z 2.215 image 0 0 0 -set atom 179 x 12.908 y 9.840 z 2.987 image 0 0 0 -set atom 180 x 12.982 y 8.641 z 2.039 image 0 0 0 -set atom 181 x 11.177 y 9.610 z 7.928 image 0 0 0 -set atom 182 x 10.443 y 10.172 z 8.053 image 0 0 0 -set atom 183 x 10.866 y 8.788 z 8.298 image 0 0 0 -set atom 184 x 1.838 y 3.206 z 15.398 image 0 0 0 -set atom 185 x 2.201 y 4.081 z 15.545 image 0 0 0 -set atom 186 x 2.117 y 2.999 z 14.422 image 0 0 0 -set atom 187 x 1.899 y 11.624 z 17.893 image 0 0 0 -set atom 188 x 1.139 y 11.678 z 17.305 image 0 0 0 -set atom 189 x 2.258 y 12.535 z 17.855 image 0 0 0 -set atom 190 x 9.220 y 13.904 z 17.340 image 0 0 0 -set atom 191 x 10.062 y 14.198 z 17.738 image 0 0 0 -set atom 192 x 9.394 y 12.999 z 17.102 image 0 0 0 -set atom 193 x 3.458 y 9.868 z 22.419 image 0 0 0 -set atom 194 x 4.398 y 10.016 z 22.654 image 0 0 0 -set atom 195 x 3.448 y 10.189 z 21.495 image 0 0 0 -set atom 196 x 15.430 y 3.274 z 7.407 image 0 0 0 -set atom 197 x 15.458 y 2.741 z 8.157 image 0 0 0 -set atom 198 x 15.933 y 2.740 z 6.770 image 0 0 0 -set atom 199 x 13.134 y 4.535 z 6.559 image 0 0 0 -set atom 200 x 12.434 y 3.932 z 6.938 image 0 0 0 -set atom 201 x 13.959 y 4.162 z 6.965 image 0 0 0 -set atom 202 x 10.295 y 14.066 z 14.320 image 0 0 0 -set atom 203 x 10.592 y 14.067 z 15.226 image 0 0 0 -set atom 204 x 9.322 y 14.226 z 14.350 image 0 0 0 -set atom 205 x 7.830 y 19.751 z 1.995 image 0 0 0 -set atom 206 x 7.257 y 19.870 z 1.247 image 0 0 0 -set atom 207 x 8.329 y 18.923 z 1.885 image 0 0 0 -set atom 208 x 15.027 y 11.249 z 9.806 image 0 0 0 -set atom 209 x 15.636 y 10.953 z 9.104 image 0 0 0 -set atom 210 x 14.929 y 12.194 z 9.545 image 0 0 0 -set atom 211 x 10.274 y 11.448 z 20.959 image 0 0 0 -set atom 212 x 10.893 y 11.073 z 21.654 image 0 0 0 -set atom 213 x 10.344 y 10.891 z 20.238 image 0 0 0 -set atom 214 x 11.473 y 6.075 z 21.702 image 0 0 0 -set atom 215 x 12.046 y 5.667 z 22.431 image 0 0 0 -set atom 216 x 10.554 y 5.939 z 22.100 image 0 0 0 -set atom 217 x 6.800 y 16.659 z 17.184 image 0 0 0 -set atom 218 x 7.143 y 16.649 z 16.327 image 0 0 0 -set atom 219 x 7.109 y 17.502 z 17.568 image 0 0 0 -set atom 220 x 14.603 y 18.110 z 3.213 image 0 0 0 -set atom 221 x 14.275 y 17.655 z 3.963 image 0 0 0 -set atom 222 x 13.842 y 18.606 z 2.878 image 0 0 0 -set atom 223 x 4.753 y 20.139 z 5.475 image 0 0 0 -set atom 224 x 4.769 y 21.053 z 5.846 image 0 0 0 -set atom 225 x 5.663 y 20.031 z 5.201 image 0 0 0 -set atom 226 x 1.615 y 17.355 z 14.355 image 0 0 0 -set atom 227 x 1.225 y 16.480 z 14.420 image 0 0 0 -set atom 228 x 0.859 y 17.984 z 14.051 image 0 0 0 -set atom 229 x 11.087 y 15.787 z 20.150 image 0 0 0 -set atom 230 x 11.221 y 14.877 z 19.698 image 0 0 0 -set atom 231 x 11.936 y 15.940 z 20.591 image 0 0 0 -set atom 232 x 9.784 y 18.060 z 16.439 image 0 0 0 -set atom 233 x 10.576 y 18.166 z 15.922 image 0 0 0 -set atom 234 x 9.941 y 18.584 z 17.234 image 0 0 0 -set atom 235 x 2.369 y 19.620 z 10.838 image 0 0 0 -set atom 236 x 2.051 y 19.425 z 11.701 image 0 0 0 -set atom 237 x 3.347 y 19.717 z 10.923 image 0 0 0 -set atom 238 x 15.158 y 15.218 z 1.453 image 0 0 0 -set atom 239 x 15.286 y 16.123 z 1.160 image 0 0 0 -set atom 240 x 14.175 y 15.219 z 1.587 image 0 0 0 -set atom 241 x 7.929 y 9.601 z 4.322 image 0 0 0 -set atom 242 x 7.364 y 10.340 z 3.912 image 0 0 0 -set atom 243 x 7.318 y 9.011 z 4.820 image 0 0 0 -set atom 244 x 11.585 y 23.121 z 19.455 image 0 0 0 -set atom 245 x 12.413 y 23.205 z 19.982 image 0 0 0 -set atom 246 x 10.816 y 23.266 z 20.095 image 0 0 0 -set atom 247 x 3.320 y 1.439 z 3.693 image 0 0 0 -set atom 248 x 3.018 y 1.263 z 2.795 image 0 0 0 -set atom 249 x 4.218 y 1.737 z 3.533 image 0 0 0 -set atom 250 x 8.378 y 22.836 z 14.074 image 0 0 0 -set atom 251 x 9.127 y 23.085 z 13.478 image 0 0 0 -set atom 252 x 7.806 y 23.652 z 14.112 image 0 0 0 -set atom 253 x 4.539 y 2.605 z 8.295 image 0 0 0 -set atom 254 x 5.460 y 2.702 z 8.123 image 0 0 0 -set atom 255 x 4.434 y 1.616 z 8.363 image 0 0 0 -set atom 256 x 8.883 y 21.581 z 5.760 image 0 0 0 -set atom 257 x 8.705 y 22.232 z 6.446 image 0 0 0 -set atom 258 x 9.357 y 22.008 z 5.077 image 0 0 0 -set atom 259 x 12.793 y 13.364 z 12.168 image 0 0 0 -set atom 260 x 12.787 y 13.548 z 11.223 image 0 0 0 -set atom 261 x 11.995 y 13.794 z 12.399 image 0 0 0 -set atom 262 x 6.667 y 7.547 z 9.646 image 0 0 0 -set atom 263 x 6.103 y 6.975 z 10.296 image 0 0 0 -set atom 264 x 7.558 y 7.292 z 10.046 image 0 0 0 -set atom 265 x 0.182 y 23.403 z 21.361 image 0 0 0 -set atom 266 x 0.301 y 23.585 z 22.346 image 0 0 0 -set atom 267 x 1.001 y 22.867 z 21.220 image 0 0 0 -set atom 268 x 11.347 y 16.007 z 23.148 image 0 0 0 -set atom 269 x 11.779 y 15.126 z 23.087 image 0 0 0 -set atom 270 x 10.586 y 15.923 z 22.581 image 0 0 0 -set atom 271 x 10.129 y 17.485 z 6.550 image 0 0 0 -set atom 272 x 9.231 y 17.467 z 6.920 image 0 0 0 -set atom 273 x 10.108 y 16.702 z 5.985 image 0 0 0 -set atom 274 x 4.654 y 5.717 z 5.023 image 0 0 0 -set atom 275 x 5.059 y 5.126 z 4.395 image 0 0 0 -set atom 276 x 5.409 y 5.785 z 5.634 image 0 0 0 -set atom 277 x 12.336 y 14.905 z 9.350 image 0 0 0 -set atom 278 x 11.849 y 15.588 z 8.883 image 0 0 0 -set atom 279 x 11.568 y 14.375 z 9.770 image 0 0 0 -set atom 280 x 5.488 y 14.255 z 13.212 image 0 0 0 -set atom 281 x 6.279 y 14.126 z 13.709 image 0 0 0 -set atom 282 x 4.864 y 13.991 z 13.878 image 0 0 0 -set atom 283 x 3.686 y 8.353 z 3.401 image 0 0 0 -set atom 284 x 4.494 y 7.930 z 3.084 image 0 0 0 -set atom 285 x 3.041 y 7.727 z 3.197 image 0 0 0 -set atom 286 x 15.005 y 14.526 z 19.133 image 0 0 0 -set atom 287 x 15.742 y 13.941 z 19.238 image 0 0 0 -set atom 288 x 14.746 y 14.453 z 18.188 image 0 0 0 -set atom 289 x 15.427 y 13.899 z 13.418 image 0 0 0 -set atom 290 x 15.598 y 14.703 z 13.915 image 0 0 0 -set atom 291 x 14.569 y 14.032 z 12.994 image 0 0 0 -set atom 292 x 15.117 y 16.342 z 15.320 image 0 0 0 -set atom 293 x 14.190 y 16.658 z 15.235 image 0 0 0 -set atom 294 x 15.725 y 17.080 z 14.950 image 0 0 0 -set atom 295 x 13.263 y 23.513 z 7.326 image 0 0 0 -set atom 296 x 14.083 y 23.900 z 7.689 image 0 0 0 -set atom 297 x 13.669 y 22.803 z 6.739 image 0 0 0 -set atom 298 x 10.030 y 11.441 z 3.434 image 0 0 0 -set atom 299 x 9.274 y 10.827 z 3.422 image 0 0 0 -set atom 300 x 10.533 y 11.362 z 2.661 image 0 0 0 -set atom 301 x 10.550 y 9.544 z 11.315 image 0 0 0 -set atom 302 x 10.055 y 10.343 z 11.396 image 0 0 0 -set atom 303 x 11.460 y 9.846 z 11.337 image 0 0 0 -set atom 304 x 2.005 y 17.796 z 21.122 image 0 0 0 -set atom 305 x 2.773 y 17.325 z 21.598 image 0 0 0 -set atom 306 x 2.173 y 18.758 z 21.265 image 0 0 0 -set atom 307 x 13.553 y 15.240 z 21.435 image 0 0 0 -set atom 308 x 14.103 y 14.959 z 20.726 image 0 0 0 -set atom 309 x 13.422 y 14.470 z 21.979 image 0 0 0 -set atom 310 x 11.456 y 2.350 z 19.585 image 0 0 0 -set atom 311 x 10.731 y 2.931 z 19.730 image 0 0 0 -set atom 312 x 11.546 y 1.862 z 20.401 image 0 0 0 -set atom 313 x 13.068 y 2.914 z 10.149 image 0 0 0 -set atom 314 x 12.803 y 2.473 z 9.295 image 0 0 0 -set atom 315 x 14.010 y 2.849 z 10.112 image 0 0 0 -set atom 316 x 5.450 y 9.067 z 5.337 image 0 0 0 -set atom 317 x 4.722 y 8.840 z 4.711 image 0 0 0 -set atom 318 x 4.939 y 8.770 z 6.117 image 0 0 0 -set atom 319 x 3.297 y 18.771 z 17.303 image 0 0 0 -set atom 320 x 3.913 y 19.272 z 17.825 image 0 0 0 -set atom 321 x 3.616 y 18.935 z 16.408 image 0 0 0 -set atom 322 x 6.597 y 15.954 z 21.463 image 0 0 0 -set atom 323 x 7.157 y 15.160 z 21.200 image 0 0 0 -set atom 324 x 7.205 y 16.451 z 22.021 image 0 0 0 -set atom 325 x 1.443 y 3.980 z 18.627 image 0 0 0 -set atom 326 x 1.536 y 3.050 z 18.247 image 0 0 0 -set atom 327 x 0.589 y 4.282 z 18.256 image 0 0 0 -set atom 328 x 3.248 y 22.876 z 3.701 image 0 0 0 -set atom 329 x 2.662 y 22.334 z 4.248 image 0 0 0 -set atom 330 x 4.106 y 22.410 z 3.781 image 0 0 0 -set atom 331 x 8.943 y 19.607 z 9.393 image 0 0 0 -set atom 332 x 9.890 y 19.666 z 9.174 image 0 0 0 -set atom 333 x 8.551 y 19.202 z 8.586 image 0 0 0 -set atom 334 x 7.534 y 23.313 z 22.010 image 0 0 0 -set atom 335 x 7.309 y 22.777 z 22.738 image 0 0 0 -set atom 336 x 6.697 y 23.403 z 21.532 image 0 0 0 -set atom 337 x 13.340 y 13.560 z 16.477 image 0 0 0 -set atom 338 x 13.400 y 13.568 z 15.542 image 0 0 0 -set atom 339 x 12.852 y 14.406 z 16.633 image 0 0 0 -set atom 340 x 8.344 y 7.845 z 20.429 image 0 0 0 -set atom 341 x 8.479 y 8.292 z 21.236 image 0 0 0 -set atom 342 x 9.102 y 8.059 z 19.900 image 0 0 0 -set atom 343 x 6.901 y 21.557 z 9.326 image 0 0 0 -set atom 344 x 7.410 y 20.744 z 9.384 image 0 0 0 -set atom 345 x 7.474 y 22.077 z 8.759 image 0 0 0 -set atom 346 x 14.403 y 7.815 z 15.212 image 0 0 0 -set atom 347 x 13.532 y 8.206 z 14.911 image 0 0 0 -set atom 348 x 14.885 y 7.681 z 14.373 image 0 0 0 -set atom 349 x 6.857 y 11.138 z 6.829 image 0 0 0 -set atom 350 x 6.107 y 11.750 z 6.800 image 0 0 0 -set atom 351 x 6.480 y 10.387 z 6.353 image 0 0 0 -set atom 352 x 10.309 y 21.500 z 11.481 image 0 0 0 -set atom 353 x 11.014 y 20.928 z 11.185 image 0 0 0 -set atom 354 x 9.595 y 20.961 z 11.183 image 0 0 0 -set atom 355 x 13.235 y 22.943 z 15.633 image 0 0 0 -set atom 356 x 12.613 y 22.525 z 16.194 image 0 0 0 -set atom 357 x 14.027 y 22.981 z 16.180 image 0 0 0 -set atom 358 x 6.818 y 20.066 z 20.150 image 0 0 0 -set atom 359 x 7.686 y 20.067 z 20.626 image 0 0 0 -set atom 360 x 6.969 y 19.869 z 19.212 image 0 0 0 -set atom 361 x 7.975 y 20.030 z 22.745 image 0 0 0 -set atom 362 x 8.632 y 20.654 z 22.435 image 0 0 0 -set atom 363 x 7.441 y 20.490 z 23.501 image 0 0 0 -set atom 364 x 12.113 y 0.921 z 4.942 image 0 0 0 -set atom 365 x 12.819 y 0.635 z 5.562 image 0 0 0 -set atom 366 x 11.814 y 1.896 z 5.223 image 0 0 0 -set atom 367 x 9.197 y 4.375 z 15.964 image 0 0 0 -set atom 368 x 9.163 y 3.590 z 15.387 image 0 0 0 -set atom 369 x 8.516 y 4.167 z 16.604 image 0 0 0 -set atom 370 x 2.421 y 3.775 z 5.058 image 0 0 0 -set atom 371 x 2.684 y 2.934 z 4.652 image 0 0 0 -set atom 372 x 3.219 y 4.340 z 5.048 image 0 0 0 -set atom 373 x 6.794 y 6.875 z 22.997 image 0 0 0 -set atom 374 x 7.166 y 7.815 z 23.093 image 0 0 0 -set atom 375 x 5.834 y 7.029 z 23.036 image 0 0 0 -set atom 376 x 11.518 y 2.141 z 14.835 image 0 0 0 -set atom 377 x 11.356 y 2.769 z 14.101 image 0 0 0 -set atom 378 x 12.345 y 1.727 z 14.583 image 0 0 0 -set atom 379 x 3.174 y 1.584 z 16.976 image 0 0 0 -set atom 380 x 2.370 y 2.077 z 16.810 image 0 0 0 -set atom 381 x 3.270 y 0.961 z 16.252 image 0 0 0 -set atom 382 x 10.848 y 10.071 z 18.631 image 0 0 0 -set atom 383 x 10.345 y 10.477 z 17.907 image 0 0 0 -set atom 384 x 11.663 y 10.551 z 18.638 image 0 0 0 -set atom 385 x 12.069 y 8.766 z 23.082 image 0 0 0 -set atom 386 x 12.023 y 9.290 z 23.888 image 0 0 0 -set atom 387 x 11.590 y 7.956 z 23.400 image 0 0 0 -set atom 388 x 5.141 y 1.611 z 0.499 image 0 0 0 -set atom 389 x 4.697 y 1.110 z 1.234 image 0 0 0 -set atom 390 x 6.031 y 1.302 z 0.586 image 0 0 0 -set atom 391 x 2.509 y 3.505 z 12.910 image 0 0 0 -set atom 392 x 2.114 y 4.138 z 12.315 image 0 0 0 -set atom 393 x 2.715 y 2.712 z 12.383 image 0 0 0 -set atom 394 x 14.354 y 1.352 z 14.004 image 0 0 0 -set atom 395 x 14.694 y 0.623 z 14.565 image 0 0 0 -set atom 396 x 14.573 y 2.195 z 14.426 image 0 0 0 -set atom 397 x 14.578 y 23.489 z 17.850 image 0 0 0 -set atom 398 x 15.476 y 23.267 z 17.861 image 0 0 0 -set atom 399 x 14.359 y 23.484 z 18.771 image 0 0 0 -set atom 400 x 5.461 y 6.754 z 1.943 image 0 0 0 -set atom 401 x 6.412 y 6.627 z 2.018 image 0 0 0 -set atom 402 x 5.209 y 5.956 z 1.434 image 0 0 0 -set atom 403 x 14.101 y 1.902 z 22.316 image 0 0 0 -set atom 404 x 14.886 y 2.398 z 22.002 image 0 0 0 -set atom 405 x 14.108 y 1.041 z 21.813 image 0 0 0 -set atom 406 x 6.142 y 11.858 z 16.052 image 0 0 0 -set atom 407 x 5.762 y 12.642 z 15.675 image 0 0 0 -set atom 408 x 5.566 y 11.146 z 15.661 image 0 0 0 -set atom 409 x 11.187 y 19.104 z 18.681 image 0 0 0 -set atom 410 x 12.029 y 18.566 z 18.863 image 0 0 0 -set atom 411 x 10.574 y 18.773 z 19.364 image 0 0 0 -set atom 412 x 11.780 y 13.509 z 0.983 image 0 0 0 -set atom 413 x 12.311 y 13.422 z 1.794 image 0 0 0 -set atom 414 x 12.379 y 13.816 z 0.300 image 0 0 0 -set atom 415 x 13.410 y 13.796 z 3.206 image 0 0 0 -set atom 416 x 12.860 y 13.342 z 3.952 image 0 0 0 -set atom 417 x 14.378 y 13.624 z 3.486 image 0 0 0 -set atom 418 x 7.314 y 0.228 z 9.152 image 0 0 0 -set atom 419 x 7.447 y 0.196 z 8.157 image 0 0 0 -set atom 420 x 8.219 y 0.336 z 9.426 image 0 0 0 -set atom 421 x 0.289 y 10.538 z 13.468 image 0 0 0 -set atom 422 x 0.286 y 10.937 z 12.602 image 0 0 0 -set atom 423 x 1.262 y 10.357 z 13.669 image 0 0 0 -set atom 424 x 12.440 y 12.407 z 5.370 image 0 0 0 -set atom 425 x 11.652 y 11.887 z 5.105 image 0 0 0 -set atom 426 x 12.893 y 11.867 z 5.977 image 0 0 0 -set atom 427 x 6.968 y 11.629 z 2.353 image 0 0 0 -set atom 428 x 6.575 y 10.896 z 1.807 image 0 0 0 -set atom 429 x 7.083 y 12.290 z 1.590 image 0 0 0 -set atom 430 x 13.533 y 10.550 z 7.160 image 0 0 0 -set atom 431 x 12.608 y 10.309 z 7.490 image 0 0 0 -set atom 432 x 14.008 y 10.940 z 7.925 image 0 0 0 -set atom 433 x 13.043 y 18.831 z 22.933 image 0 0 0 -set atom 434 x 13.439 y 17.936 z 22.986 image 0 0 0 -set atom 435 x 12.139 y 18.764 z 23.145 image 0 0 0 -set atom 436 x 11.706 y 15.811 z 16.829 image 0 0 0 -set atom 437 x 10.892 y 16.347 z 16.590 image 0 0 0 -set atom 438 x 12.344 y 16.466 z 17.162 image 0 0 0 -set atom 439 x 11.642 y 19.030 z 4.866 image 0 0 0 -set atom 440 x 10.752 y 18.786 z 5.209 image 0 0 0 -set atom 441 x 11.534 y 19.147 z 3.897 image 0 0 0 -set atom 442 x 13.550 y 21.522 z 9.565 image 0 0 0 -set atom 443 x 13.279 y 21.744 z 8.655 image 0 0 0 -set atom 444 x 13.859 y 22.419 z 9.914 image 0 0 0 -set atom 445 x 12.001 y 20.877 z 14.108 image 0 0 0 -set atom 446 x 12.060 y 21.566 z 14.774 image 0 0 0 -set atom 447 x 11.186 y 21.104 z 13.629 image 0 0 0 -set atom 448 x 12.814 y 17.906 z 7.383 image 0 0 0 -set atom 449 x 13.379 y 17.410 z 6.688 image 0 0 0 -set atom 450 x 11.963 y 17.994 z 6.954 image 0 0 0 -set atom 451 x 15.989 y 19.751 z 4.862 image 0 0 0 -set atom 452 x 15.952 y 20.632 z 4.460 image 0 0 0 -set atom 453 x 15.557 y 19.210 z 4.188 image 0 0 0 -set atom 454 x 10.963 y 1.737 z 11.790 image 0 0 0 -set atom 455 x 10.319 y 2.240 z 11.334 image 0 0 0 -set atom 456 x 11.709 y 2.167 z 11.210 image 0 0 0 -set atom 457 x 5.526 y 8.369 z 14.858 image 0 0 0 -set atom 458 x 4.950 y 8.218 z 14.072 image 0 0 0 -set atom 459 x 4.945 y 8.919 z 15.363 image 0 0 0 -set atom 460 x 14.776 y 4.939 z 12.443 image 0 0 0 -set atom 461 x 14.636 y 5.952 z 12.252 image 0 0 0 -set atom 462 x 13.865 y 4.712 z 12.604 image 0 0 0 -set atom 463 x 7.529 y 4.508 z 1.396 image 0 0 0 -set atom 464 x 8.313 y 4.582 z 0.857 image 0 0 0 -set atom 465 x 6.783 y 4.511 z 0.768 image 0 0 0 -set atom 466 x 11.435 y 0.836 z 22.059 image 0 0 0 -set atom 467 x 11.858 y 0.103 z 21.657 image 0 0 0 -set atom 468 x 12.219 y 1.281 z 22.508 image 0 0 0 -set atom 469 x 11.200 y 4.151 z 3.471 image 0 0 0 -set atom 470 x 12.053 y 4.360 z 3.928 image 0 0 0 -set atom 471 x 10.572 y 4.426 z 4.138 image 0 0 0 -set atom 472 x 4.884 y 4.081 z 13.713 image 0 0 0 -set atom 473 x 4.970 y 4.746 z 14.373 image 0 0 0 -set atom 474 x 3.932 y 3.975 z 13.593 image 0 0 0 -set atom 475 x 13.867 y 4.624 z 3.954 image 0 0 0 -set atom 476 x 14.067 y 4.641 z 4.904 image 0 0 0 -set atom 477 x 14.122 y 5.494 z 3.648 image 0 0 0 -set atom 478 x 3.174 y 11.159 z 5.954 image 0 0 0 -set atom 479 x 3.904 y 11.073 z 5.352 image 0 0 0 -set atom 480 x 3.204 y 12.104 z 6.129 image 0 0 0 -set atom 481 x 12.922 y 2.911 z 17.412 image 0 0 0 -set atom 482 x 12.421 y 2.431 z 18.089 image 0 0 0 -set atom 483 x 12.240 y 2.996 z 16.701 image 0 0 0 -set atom 484 x 13.644 y 7.961 z 20.946 image 0 0 0 -set atom 485 x 13.183 y 7.158 z 20.680 image 0 0 0 -set atom 486 x 13.018 y 8.315 z 21.687 image 0 0 0 -set atom 487 x 6.612 y 3.396 z 17.042 image 0 0 0 -set atom 488 x 6.138 y 2.987 z 17.830 image 0 0 0 -set atom 489 x 6.248 y 2.883 z 16.306 image 0 0 0 -set atom 490 x 3.628 y 15.453 z 9.684 image 0 0 0 -set atom 491 x 3.604 y 16.368 z 9.365 image 0 0 0 -set atom 492 x 3.266 y 15.478 z 10.592 image 0 0 0 -set atom 493 x 1.641 y 18.264 z 8.136 image 0 0 0 -set atom 494 x 0.755 y 18.490 z 8.008 image 0 0 0 -set atom 495 x 1.981 y 19.003 z 8.665 image 0 0 0 -set atom 496 x 8.716 y 0.819 z 21.571 image 0 0 0 -set atom 497 x 8.359 y 0.399 z 22.460 image 0 0 0 -set atom 498 x 9.622 y 1.046 z 21.690 image 0 0 0 -set atom 499 x 14.269 y 10.001 z 4.369 image 0 0 0 -set atom 500 x 14.973 y 10.528 z 4.752 image 0 0 0 -set atom 501 x 13.690 y 9.859 z 5.092 image 0 0 0 -set atom 502 x 14.691 y 13.817 z 9.050 image 0 0 0 -set atom 503 x 15.162 y 14.372 z 8.385 image 0 0 0 -set atom 504 x 13.821 y 14.250 z 9.113 image 0 0 0 -set atom 505 x 12.273 y 5.424 z 10.404 image 0 0 0 -set atom 506 x 12.384 y 4.472 z 10.210 image 0 0 0 -set atom 507 x 13.153 y 5.714 z 10.501 image 0 0 0 -set atom 508 x 3.759 y 13.253 z 15.143 image 0 0 0 -set atom 509 x 3.552 y 13.546 z 16.059 image 0 0 0 -set atom 510 x 2.862 y 13.321 z 14.740 image 0 0 0 -set atom 511 x 7.319 y 14.432 z 15.015 image 0 0 0 -set atom 512 x 7.633 y 15.319 z 14.742 image 0 0 0 -set atom 513 x 7.702 y 14.303 z 15.933 image 0 0 0 -set atom 514 x 3.117 y 11.819 z 10.070 image 0 0 0 -set atom 515 x 3.490 y 12.496 z 9.523 image 0 0 0 -set atom 516 x 3.937 y 11.583 z 10.539 image 0 0 0 -set atom 517 x 0.549 y 16.393 z 10.366 image 0 0 0 -set atom 518 x 1.292 y 16.322 z 11.016 image 0 0 0 -set atom 519 x 0.665 y 17.283 z 9.972 image 0 0 0 -set atom 520 x 10.050 y 5.605 z 5.758 image 0 0 0 -set atom 521 x 10.155 y 6.554 z 5.556 image 0 0 0 -set atom 522 x 10.797 y 5.389 z 6.309 image 0 0 0 -set atom 523 x 7.881 y 3.518 z 5.700 image 0 0 0 -set atom 524 x 8.550 y 4.225 z 5.812 image 0 0 0 -set atom 525 x 7.070 y 3.834 z 6.169 image 0 0 0 -set atom 526 x 8.559 y 3.515 z 11.535 image 0 0 0 -set atom 527 x 8.435 y 4.298 z 12.155 image 0 0 0 -set atom 528 x 7.955 y 2.899 z 11.952 image 0 0 0 -set atom 529 x 13.039 y 10.511 z 11.777 image 0 0 0 -set atom 530 x 13.825 y 10.589 z 11.282 image 0 0 0 -set atom 531 x 12.883 y 11.473 z 11.916 image 0 0 0 -set atom 532 x 15.316 y 3.976 z 15.033 image 0 0 0 -set atom 533 x 15.353 y 4.265 z 14.065 image 0 0 0 -set atom 534 x 14.585 y 4.533 z 15.460 image 0 0 0 -set atom 535 x 8.400 y 5.552 z 13.557 image 0 0 0 -set atom 536 x 9.070 y 5.240 z 14.185 image 0 0 0 -set atom 537 x 7.739 y 5.945 z 14.163 image 0 0 0 -set atom 538 x 4.281 y 21.161 z 19.066 image 0 0 0 -set atom 539 x 5.157 y 21.058 z 19.381 image 0 0 0 -set atom 540 x 4.169 y 22.110 z 18.904 image 0 0 0 -set atom 541 x 13.870 y 7.474 z 12.187 image 0 0 0 -set atom 542 x 13.209 y 8.073 z 12.633 image 0 0 0 -set atom 543 x 14.457 y 8.029 z 11.659 image 0 0 0 -set atom 544 x 13.600 y 17.247 z 9.998 image 0 0 0 -set atom 545 x 13.256 y 16.385 z 10.107 image 0 0 0 -set atom 546 x 13.616 y 17.337 z 9.047 image 0 0 0 -set atom 547 x 10.099 y 18.083 z 21.099 image 0 0 0 -set atom 548 x 10.453 y 17.258 z 20.699 image 0 0 0 -set atom 549 x 9.398 y 17.746 z 21.690 image 0 0 0 -set atom 550 x 15.465 y 7.955 z 17.814 image 0 0 0 -set atom 551 x 15.150 y 7.979 z 16.932 image 0 0 0 -set atom 552 x 14.706 y 7.563 z 18.306 image 0 0 0 -set atom 553 x 9.016 y 4.086 z 8.814 image 0 0 0 -set atom 554 x 9.377 y 5.001 z 8.813 image 0 0 0 -set atom 555 x 8.726 y 3.741 z 9.661 image 0 0 0 -set atom 556 x 6.439 y 5.144 z 7.455 image 0 0 0 -set atom 557 x 7.310 y 4.836 z 7.837 image 0 0 0 -set atom 558 x 6.121 y 5.819 z 8.116 image 0 0 0 -set atom 559 x 13.331 y 4.563 z 23.416 image 0 0 0 -set atom 560 x 14.315 y 4.772 z 23.360 image 0 0 0 -set atom 561 x 13.215 y 3.678 z 23.134 image 0 0 0 -set atom 562 x 11.401 y 21.480 z 17.136 image 0 0 0 -set atom 563 x 11.522 y 22.112 z 17.856 image 0 0 0 -set atom 564 x 11.255 y 20.672 z 17.636 image 0 0 0 -set atom 565 x 12.076 y 4.645 z 13.566 image 0 0 0 -set atom 566 x 12.000 y 5.522 z 13.148 image 0 0 0 -set atom 567 x 11.827 y 4.835 z 14.443 image 0 0 0 -set atom 568 x 9.131 y 1.075 z 15.841 image 0 0 0 -set atom 569 x 9.948 y 1.463 z 15.412 image 0 0 0 -set atom 570 x 9.113 y 0.161 z 15.464 image 0 0 0 -set atom 571 x 7.694 y 8.338 z 16.687 image 0 0 0 -set atom 572 x 7.323 y 8.081 z 17.508 image 0 0 0 -set atom 573 x 6.991 y 8.476 z 16.072 image 0 0 0 -set atom 574 x 11.912 y 13.212 z 19.726 image 0 0 0 -set atom 575 x 12.854 y 13.225 z 19.881 image 0 0 0 -set atom 576 x 11.504 y 12.764 z 20.555 image 0 0 0 -set atom 577 x 5.115 y 19.820 z 22.632 image 0 0 0 -set atom 578 x 4.270 y 19.752 z 22.092 image 0 0 0 -set atom 579 x 5.800 y 19.585 z 21.996 image 0 0 0 -set atom 580 x 14.170 y 23.047 z 20.478 image 0 0 0 -set atom 581 x 15.015 y 22.883 z 20.902 image 0 0 0 -set atom 582 x 13.757 y 22.177 z 20.579 image 0 0 0 -set atom 583 x 13.163 y 20.489 z 20.636 image 0 0 0 -set atom 584 x 12.450 y 20.171 z 20.104 image 0 0 0 -set atom 585 x 13.220 y 19.875 z 21.393 image 0 0 0 -set atom 586 x 11.316 y 2.273 z 7.956 image 0 0 0 -set atom 587 x 11.391 y 1.358 z 8.151 image 0 0 0 -set atom 588 x 10.423 y 2.479 z 8.181 image 0 0 0 -set atom 589 x 10.407 y 6.649 z 8.888 image 0 0 0 -set atom 590 x 9.810 y 7.215 z 9.386 image 0 0 0 -set atom 591 x 11.077 y 6.417 z 9.547 image 0 0 0 -set atom 592 x 7.574 y 19.420 z 4.717 image 0 0 0 -set atom 593 x 7.704 y 19.335 z 3.679 image 0 0 0 -set atom 594 x 7.970 y 20.255 z 4.957 image 0 0 0 -set atom 595 x 12.254 y 19.676 z 2.229 image 0 0 0 -set atom 596 x 12.678 y 20.538 z 2.358 image 0 0 0 -set atom 597 x 12.115 y 19.535 z 1.250 image 0 0 0 -set atom 598 x 14.036 y 7.730 z 6.644 image 0 0 0 -set atom 599 x 14.358 y 7.138 z 7.346 image 0 0 0 -set atom 600 x 13.886 y 8.589 z 7.123 image 0 0 0 -set atom 601 x 8.900 y 7.310 z 11.290 image 0 0 0 -set atom 602 x 8.739 y 6.706 z 12.078 image 0 0 0 -set atom 603 x 9.555 y 8.003 z 11.531 image 0 0 0 -set atom 604 x 9.495 y 14.416 z 1.979 image 0 0 0 -set atom 605 x 10.354 y 14.203 z 1.548 image 0 0 0 -set atom 606 x 9.165 y 13.566 z 2.099 image 0 0 0 -set atom 607 x 13.605 y 5.353 z 19.280 image 0 0 0 -set atom 608 x 13.658 y 4.527 z 18.812 image 0 0 0 -set atom 609 x 12.688 y 5.367 z 19.516 image 0 0 0 -set atom 610 x 7.334 y 17.973 z 7.090 image 0 0 0 -set atom 611 x 7.571 y 18.390 z 6.200 image 0 0 0 -set atom 612 x 6.533 y 17.444 z 6.885 image 0 0 0 -set atom 613 x 13.912 y 11.040 z 17.383 image 0 0 0 -set atom 614 x 13.913 y 10.932 z 16.423 image 0 0 0 -set atom 615 x 13.612 y 11.935 z 17.518 image 0 0 0 -set atom 616 x 14.682 y 11.334 z 14.388 image 0 0 0 -set atom 617 x 15.236 y 11.941 z 13.876 image 0 0 0 -set atom 618 x 14.266 y 10.683 z 13.763 image 0 0 0 -set atom 619 x 12.414 y 9.004 z 13.909 image 0 0 0 -set atom 620 x 11.523 y 8.931 z 14.184 image 0 0 0 -set atom 621 x 12.375 y 9.766 z 13.286 image 0 0 0 -set atom 622 x 15.898 y 3.293 z 1.648 image 0 0 0 -set atom 623 x 15.837 y 3.977 z 2.359 image 0 0 0 -set atom 624 x 15.065 y 2.796 z 1.789 image 0 0 0 -set atom 625 x 3.080 y 0.949 z 11.788 image 0 0 0 -set atom 626 x 3.690 y 0.500 z 11.172 image 0 0 0 -set atom 627 x 2.196 y 0.556 z 11.641 image 0 0 0 -set atom 628 x 0.897 y 12.813 z 20.940 image 0 0 0 -set atom 629 x 1.234 y 13.577 z 21.489 image 0 0 0 -set atom 630 x 1.110 y 12.083 z 21.442 image 0 0 0 -set atom 631 x 6.255 y 9.802 z 0.364 image 0 0 0 -set atom 632 x 6.954 y 9.121 z 0.671 image 0 0 0 -set atom 633 x 5.459 y 9.264 z 0.196 image 0 0 0 -set atom 634 x 6.140 y 3.669 z 3.704 image 0 0 0 -set atom 635 x 6.732 y 3.837 z 2.949 image 0 0 0 -set atom 636 x 6.807 y 3.408 z 4.378 image 0 0 0 -set atom 637 x 5.150 y 11.685 z 11.994 image 0 0 0 -set atom 638 x 5.312 y 12.641 z 12.020 image 0 0 0 -set atom 639 x 5.614 y 11.405 z 12.778 image 0 0 0 -set atom 640 x 5.196 y 19.304 z 15.315 image 0 0 0 -set atom 641 x 5.227 y 20.213 z 14.942 image 0 0 0 -set atom 642 x 5.252 y 18.720 z 14.569 image 0 0 0 -set atom 643 x 2.179 y 13.464 z 7.177 image 0 0 0 -set atom 644 x 2.719 y 14.061 z 7.737 image 0 0 0 -set atom 645 x 1.640 y 13.021 z 7.843 image 0 0 0 -set atom 646 x 1.926 y 21.439 z 17.027 image 0 0 0 -set atom 647 x 2.672 y 21.817 z 16.545 image 0 0 0 -set atom 648 x 2.398 y 20.912 z 17.662 image 0 0 0 -set atom 649 x 0.688 y 2.781 z 7.114 image 0 0 0 -set atom 650 x 1.488 y 3.190 z 6.703 image 0 0 0 -set atom 651 x 0.053 y 3.429 z 6.930 image 0 0 0 -set atom 652 x 0.449 y 7.366 z 9.140 image 0 0 0 -set atom 653 x 0.202 y 6.479 z 9.095 image 0 0 0 -set atom 654 x 0.796 y 7.563 z 8.256 image 0 0 0 -set atom 655 x 0.913 y 12.320 z 0.937 image 0 0 0 -set atom 656 x 0.623 y 11.700 z 0.268 image 0 0 0 -set atom 657 x 1.290 y 11.784 z 1.628 image 0 0 0 -set atom 658 x 7.889 y 16.997 z 14.360 image 0 0 0 -set atom 659 x 7.935 y 17.181 z 13.358 image 0 0 0 -set atom 660 x 8.602 y 17.562 z 14.734 image 0 0 0 -set atom 661 x 3.230 y 22.882 z 11.736 image 0 0 0 -set atom 662 x 3.601 y 21.950 z 11.670 image 0 0 0 -set atom 663 x 2.861 y 22.992 z 10.853 image 0 0 0 -set atom 664 x 4.620 y 22.335 z 7.130 image 0 0 0 -set atom 665 x 3.754 y 22.591 z 7.590 image 0 0 0 -set atom 666 x 5.178 y 22.349 z 7.907 image 0 0 0 -set atom 667 x 1.124 y 22.962 z 13.514 image 0 0 0 -set atom 668 x 1.837 y 22.901 z 12.860 image 0 0 0 -set atom 669 x 0.685 y 23.799 z 13.310 image 0 0 0 -set atom 670 x 8.561 y 10.924 z 16.881 image 0 0 0 -set atom 671 x 7.916 y 11.188 z 16.202 image 0 0 0 -set atom 672 x 8.309 y 10.008 z 17.123 image 0 0 0 -set atom 673 x 4.751 y 19.009 z 2.814 image 0 0 0 -set atom 674 x 4.754 y 18.978 z 3.760 image 0 0 0 -set atom 675 x 5.300 y 18.306 z 2.612 image 0 0 0 -set atom 676 x 3.406 y 0.117 z 14.493 image 0 0 0 -set atom 677 x 3.348 y 0.244 z 13.546 image 0 0 0 -set atom 678 x 4.378 y 0.190 z 14.724 image 0 0 0 -set atom 679 x 2.278 y 3.922 z 1.200 image 0 0 0 -set atom 680 x 2.701 y 3.392 z 0.560 image 0 0 0 -set atom 681 x 1.556 y 3.406 z 1.415 image 0 0 0 -set atom 682 x 6.246 y 21.216 z 13.564 image 0 0 0 -set atom 683 x 7.127 y 21.533 z 13.794 image 0 0 0 -set atom 684 x 5.802 y 22.075 z 13.455 image 0 0 0 -set atom 685 x 5.348 y 15.459 z 5.988 image 0 0 0 -set atom 686 x 4.942 y 16.211 z 6.465 image 0 0 0 -set atom 687 x 4.964 y 14.679 z 6.422 image 0 0 0 -set atom 688 x 1.312 y 13.577 z 13.829 image 0 0 0 -set atom 689 x 1.594 y 13.350 z 12.963 image 0 0 0 -set atom 690 x 0.905 y 14.443 z 13.634 image 0 0 0 -set atom 691 x 10.395 y 21.375 z 22.397 image 0 0 0 -set atom 692 x 10.900 y 20.680 z 22.794 image 0 0 0 -set atom 693 x 10.682 y 22.154 z 22.828 image 0 0 0 -set atom 694 x 6.013 y 16.085 z 3.326 image 0 0 0 -set atom 695 x 6.016 y 16.035 z 4.292 image 0 0 0 -set atom 696 x 5.249 y 15.516 z 3.046 image 0 0 0 -set atom 697 x 2.184 y 22.110 z 9.500 image 0 0 0 -set atom 698 x 1.913 y 21.297 z 9.998 image 0 0 0 -set atom 699 x 1.389 y 22.233 z 8.964 image 0 0 0 -set atom 700 x 3.207 y 13.979 z 17.772 image 0 0 0 -set atom 701 x 3.947 y 14.082 z 18.373 image 0 0 0 -set atom 702 x 2.585 y 14.685 z 17.921 image 0 0 0 -set atom 703 x 13.639 y 16.098 z 5.269 image 0 0 0 -set atom 704 x 14.099 y 15.394 z 4.872 image 0 0 0 -set atom 705 x 12.755 y 15.724 z 5.343 image 0 0 0 -set atom 706 x 1.981 y 16.635 z 18.663 image 0 0 0 -set atom 707 x 1.921 y 17.181 z 19.529 image 0 0 0 -set atom 708 x 2.656 y 17.117 z 18.156 image 0 0 0 -set atom 709 x 13.457 y 20.491 z 6.545 image 0 0 0 -set atom 710 x 13.544 y 19.713 z 6.959 image 0 0 0 -set atom 711 x 13.199 y 20.170 z 5.601 image 0 0 0 -set atom 712 x 3.438 y 8.099 z 0.316 image 0 0 0 -set atom 713 x 2.547 y 7.847 z 0.577 image 0 0 0 -set atom 714 x 3.889 y 7.775 z 1.093 image 0 0 0 -set atom 715 x 9.016 y 15.690 z 9.485 image 0 0 0 -set atom 716 x 9.158 y 14.769 z 9.701 image 0 0 0 -set atom 717 x 8.537 y 15.554 z 8.652 image 0 0 0 -set atom 718 x 1.562 y 6.536 z 12.239 image 0 0 0 -set atom 719 x 0.960 y 7.250 z 12.049 image 0 0 0 -set atom 720 x 1.197 y 5.827 z 11.553 image 0 0 0 -set atom 721 x 1.314 y 9.385 z 7.173 image 0 0 0 -set atom 722 x 1.333 y 8.706 z 6.444 image 0 0 0 -set atom 723 x 2.056 y 9.953 z 6.980 image 0 0 0 -set atom 724 x 7.572 y 0.420 z 3.478 image 0 0 0 -set atom 725 x 7.636 y 0.339 z 2.503 image 0 0 0 -set atom 726 x 6.628 y 0.234 z 3.530 image 0 0 0 -set atom 727 x 1.133 y 7.080 z 5.078 image 0 0 0 -set atom 728 x 1.201 y 7.102 z 4.137 image 0 0 0 -set atom 729 x 0.358 y 6.549 z 5.302 image 0 0 0 -set atom 730 x 11.515 y 22.342 z 4.827 image 0 0 0 -set atom 731 x 10.875 y 21.911 z 4.185 image 0 0 0 -set atom 732 x 11.205 y 21.919 z 5.694 image 0 0 0 -set atom 733 x 5.279 y 5.755 z 11.457 image 0 0 0 -set atom 734 x 4.504 y 5.333 z 10.967 image 0 0 0 -set atom 735 x 5.564 y 4.986 z 12.019 image 0 0 0 -set atom 736 x 8.890 y 21.041 z 16.070 image 0 0 0 -set atom 737 x 8.698 y 21.572 z 15.300 image 0 0 0 -set atom 738 x 9.800 y 21.340 z 16.244 image 0 0 0 -set atom 739 x 6.000 y 11.283 z 22.324 image 0 0 0 -set atom 740 x 5.866 y 12.057 z 22.939 image 0 0 0 -set atom 741 x 5.863 y 11.634 z 21.452 image 0 0 0 -set atom 742 x 7.834 y 14.408 z 7.527 image 0 0 0 -set atom 743 x 7.105 y 14.717 z 6.993 image 0 0 0 -set atom 744 x 8.194 y 13.714 z 6.926 image 0 0 0 -set atom 745 x 5.667 y 11.812 z 19.542 image 0 0 0 -set atom 746 x 5.647 y 12.743 z 19.497 image 0 0 0 -set atom 747 x 5.889 y 11.629 z 18.618 image 0 0 0 -set atom 748 x 12.997 y 18.576 z 15.207 image 0 0 0 -set atom 749 x 12.617 y 19.193 z 14.493 image 0 0 0 -set atom 750 x 13.582 y 19.163 z 15.737 image 0 0 0 -set atom 751 x 0.675 y 11.574 z 10.952 image 0 0 0 -set atom 752 x 1.597 y 11.546 z 10.574 image 0 0 0 -set atom 753 x 0.265 y 12.150 z 10.339 image 0 0 0 -set atom 754 x 8.782 y 17.187 z 2.362 image 0 0 0 -set atom 755 x 8.004 y 16.786 z 2.797 image 0 0 0 -set atom 756 x 9.140 y 16.422 z 1.970 image 0 0 0 -set atom 757 x 2.113 y 6.516 z 21.893 image 0 0 0 -set atom 758 x 2.170 y 5.576 z 22.160 image 0 0 0 -set atom 759 x 2.446 y 6.949 z 22.707 image 0 0 0 -set atom 760 x 2.583 y 16.123 z 12.046 image 0 0 0 -set atom 761 x 3.491 y 16.508 z 12.059 image 0 0 0 -set atom 762 x 2.312 y 16.312 z 12.887 image 0 0 0 -set atom 763 x 2.246 y 20.883 z 4.995 image 0 0 0 -set atom 764 x 1.611 y 20.097 z 4.885 image 0 0 0 -set atom 765 x 3.079 y 20.473 z 5.195 image 0 0 0 -set atom 766 x 8.156 y 17.564 z 11.520 image 0 0 0 -set atom 767 x 8.355 y 18.345 z 10.921 image 0 0 0 -set atom 768 x 8.334 y 16.820 z 10.874 image 0 0 0 -set atom 769 x 2.915 y 14.197 z 3.393 image 0 0 0 -set atom 770 x 2.155 y 14.414 z 3.916 image 0 0 0 -set atom 771 x 2.719 y 13.333 z 3.011 image 0 0 0 -set atom 772 x 8.578 y 0.832 z 6.351 image 0 0 0 -set atom 773 x 7.928 y 0.530 z 5.693 image 0 0 0 -set atom 774 x 8.563 y 1.801 z 6.335 image 0 0 0 -set atom 775 x 7.287 y 10.172 z 13.815 image 0 0 0 -set atom 776 x 6.631 y 9.473 z 14.077 image 0 0 0 -set atom 777 x 8.119 y 9.669 z 13.852 image 0 0 0 -set atom 778 x 3.347 y 10.487 z 19.814 image 0 0 0 -set atom 779 x 2.792 y 10.955 z 19.188 image 0 0 0 -set atom 780 x 4.264 y 10.639 z 19.456 image 0 0 0 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.init b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.init deleted file mode 100644 index d01b26e206..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.init +++ /dev/null @@ -1,9 +0,0 @@ - # -- 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 diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.settings b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.settings deleted file mode 100644 index ba1d4626c1..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.in.settings +++ /dev/null @@ -1,7 +0,0 @@ - bond_coeff 1 harmonic 200.0 1.0 - angle_coeff 1 harmonic 200.0 109.47 - pair_coeff 1 1 lj/charmm/coul/long 0.1553 3.166 - pair_coeff 2 2 lj/charmm/coul/long 0.0 2.058 - group spce type 1 2 - fix fSHAKE all shake 0.0001 10 100 b 1 a 1 - # (Remember to "unfix" fSHAKE during minimization.) diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt deleted file mode 100644 index dc77da51f0..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/moltemplate_files/system.lt +++ /dev/null @@ -1,25 +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 ice_wat32.pdb system.lt") -# -############################# COMMENTS: #################################### -# Alternately, you can specify a lattice of water molecules this way: -# wat = new SPCE [10].move(0,0,3.6) -# [10].move(0,3.6,0) -# [10].move(3.6,0,0) -# -# ...and specify the periodic boundary conditions this way: -#write_once("PBC") { -# 0.0 36.00 xlo xhi -# 0.0 36.00 ylo yhi -# 0.0 36.00 zlo zhi -#} -############################################################################## diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.min b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.min deleted file mode 100644 index ea100b01e2..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.min +++ /dev/null @@ -1,18 +0,0 @@ -################################################## -# Box of water -################################################## -# -# define the system being simulated: - -include "system.in" - -dump 1 all custom 100 traj_min.lammpstrj id mol type x y z ix iy iz - -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-4 1.0e-6 500 2000 - -# (For a system with ~6000 atoms, this takes 1-4 minutes on a i7 720 processor.) -# Alternate (faster) minimizer settings (about 10 sec): - -write_restart system_after_min.rst diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.npt deleted file mode 100644 index 7cee108bc5..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.npt +++ /dev/null @@ -1,33 +0,0 @@ -################################################## -# Box of water -################################################## -# -# define the system being simulated: - -# -- init section -- -include system.in.init - -# -- atom definition section -- - -#read_data system.data -read_restart system_after_min.rst - -# -- settings section -- -include system.in.settings - -# -- run section -- - -# Note: It is possible to use a 2.0 timestep with SPCE water, -# if you start from a reasonable starting structure. -# However during equilibration I often set it to 1.0 to be safe. -timestep 1.0 - -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 10000 - -write_restart system_after_npt.rst diff --git a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.nvt deleted file mode 100644 index b4c7088db1..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/convert_PDB_to_LT_examples/waterSPCE_from_PDBfile/run.in.nvt +++ /dev/null @@ -1,38 +0,0 @@ -################################################## -# Box of water -################################################## -# -# define the system being simulated: - -# -- init section -- -include system.in.init - -# -- atom definition section -- - -#read_data system.data -#read_restart system_after_min.rst -read_restart system_after_npt.rst - -# -- settings section -- -include system.in.settings - -# -- run section -- - -timestep 2.0 - -dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz -#dump 1 all dcd 100 traj_nvt.dcd -#dump_modify unwrap yes -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 1000000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README.TXT b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README.TXT deleted file mode 100644 index 1a077178e3..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/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/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh deleted file mode 100755 index e8e13dec72..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_run.sh +++ /dev/null @@ -1,19 +0,0 @@ -# This is just an example. -# -# Note: The "run.in.nvt" file is a LAMMPS input script which attempts to read -# the input scripts and data files you created with 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.nvt - -# Alternately, if you have MPI installed, try something like this: - -#NUMPROCS=4 -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_setup.sh deleted file mode 100755 index acc5fbbaad..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/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/heteropolymer_melt_attempt1/README_visualise.txt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/README_visualise.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/heteropolymer_melt_attempt1/images/zoom1_rainbow_t=0ps_LR.jpg b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/images/zoom1_rainbow_t=0ps_LR.jpg deleted file mode 100644 index a7876c0e0a..0000000000 Binary files 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b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/monomers.lt deleted file mode 100644 index af043b39ed..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/monomers.lt +++ /dev/null @@ -1,125 +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 { - - - PVDF { - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C1 $mol:... @atom:../C 0.0 -1.000 0.4000 0.00000 - $atom:H1 $mol:... @atom:../RH 0.0 -1.000 1.000 1.000 - $atom:H2 $mol:... @atom:../RH 0.0 -1.000 1.000 -1.000 - $atom:C2 $mol:... @atom:../C 0.0 1.000 -0.4000 0.00000 - $atom:F1 $mol:... @atom:../RF 0.0 1.000 -1.000 1.000 - $atom:F2 $mol:... @atom:../RF 0.0 1.000 -1.000 -1.000 - } - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:C1R1 @bond:../sidechain $atom:C1 $atom:H1 - $bond:C1R2 @bond:../sidechain $atom:C1 $atom:H2 - $bond:C2R1 @bond:../sidechain $atom:C2 $atom:F1 - $bond:C2R2 @bond:../sidechain $atom:C2 $atom:F2 - $bond:C12 @bond:../bb $atom:C1 $atom:C2 - } - } # PVDF - - - PCTFE { - # atom-id mol-id atom-type charge x y z - - write("Data Atoms") { - $atom:C1 $mol:... @atom:../C 0.0 -1.000 0.4000 0.00000 - $atom:F1 $mol:... @atom:../RF 0.0 -1.000 1.000 1.000 - $atom:F2 $mol:... @atom:../RF 0.0 -1.000 1.000 -1.000 - $atom:C2 $mol:... @atom:../C 0.0 1.000 -0.4000 0.00000 - $atom:F3 $mol:... @atom:../RF 0.0 1.000 -1.000 1.000 - $atom:CL $mol:... @atom:../RCl 0.0 1.000 -1.000 -1.000 - } - - # bond-id bond-type atom-id1 atom-id2 - - write("Data Bonds") { - $bond:C1R1 @bond:../sidechain $atom:C1 $atom:F1 - $bond:C1R2 @bond:../sidechain $atom:C1 $atom:F2 - $bond:C2R1 @bond:../sidechain $atom:C2 $atom:F3 - $bond:C2R2 @bond:../sidechain $atom:C2 $atom:CL - $bond:C12 @bond:../bb $atom:C1 $atom:C2 - } - } # PCTFE - - - # atom-type mass - - write_once("Data Masses") { - @atom:C 12.0 - @atom:RH 1.0 - @atom:RF 19.0 - @atom:RCl 35.453 - } - - - # atom-type atom-type epsilon sigma - - write_once("In Settings") { - pair_coeff @atom:C @atom:C 0.20 2.0 - pair_coeff @atom:RH @atom:RH 0.20 1.0 - pair_coeff @atom:RF @atom:RF 0.40 2.0 - pair_coeff @atom:RCl @atom:RCl 0.40 2.0 - } - - - # bond-type k r0 - - write_once("Data Bond Coeffs") { - @bond:sidechain 30.0 1.2 - @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. - - # angle-type k theta0 - - write_once("Data Angle Coeffs") { - @angle:backbone 50.00 160 - @angle:sidechain 50.00 120 - @angle:RCR 50.00 120 - } - - # dihedral-type K1 K2 K3 K4 - - write_once("Data Dihedral Coeffs") { - @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:C @atom:C @atom:C @bond:* @bond:* - @angle:sidechain @atom:C @atom:C @atom:R* @bond:* @bond:* - @angle:RCR @atom:R* @atom:C @atom:R* @bond:* @bond:* - } - - # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3 - - write_once("Data Dihedrals By Type") { - @dihedral:backbn @atom:C @atom:C @atom:C @atom:C @bond:* @bond:* @bond:* - } - -} # MonomerTypes diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt deleted file mode 100644 index 27d1c16b0d..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/polymer.lt +++ /dev/null @@ -1,231 +0,0 @@ -import "monomers.lt" - -using namespace MonomerTypes - -Polymer200 { - - # Make a chain of monomers with random composition: - - monomers = new random([PVDF,PCTFE], [0.25,0.75]) [200].move(4.0, 0, 0) - - # Now, link the monomers together this way: - write("Data Bonds") { - $bond:bb1 @bond:MonomerTypes/bb $atom:monomers[0]/C2 $atom:monomers[1]/C1 - $bond:bb2 @bond:MonomerTypes/bb $atom:monomers[1]/C2 $atom:monomers[2]/C1 - $bond:bb3 @bond:MonomerTypes/bb $atom:monomers[2]/C2 $atom:monomers[3]/C1 - $bond:bb4 @bond:MonomerTypes/bb $atom:monomers[3]/C2 $atom:monomers[4]/C1 - $bond:bb5 @bond:MonomerTypes/bb $atom:monomers[4]/C2 $atom:monomers[5]/C1 - $bond:bb6 @bond:MonomerTypes/bb $atom:monomers[5]/C2 $atom:monomers[6]/C1 - $bond:bb7 @bond:MonomerTypes/bb $atom:monomers[6]/C2 $atom:monomers[7]/C1 - $bond:bb8 @bond:MonomerTypes/bb $atom:monomers[7]/C2 $atom:monomers[8]/C1 - $bond:bb9 @bond:MonomerTypes/bb $atom:monomers[8]/C2 $atom:monomers[9]/C1 - $bond:bb10 @bond:MonomerTypes/bb $atom:monomers[9]/C2 $atom:monomers[10]/C1 - $bond:bb11 @bond:MonomerTypes/bb $atom:monomers[10]/C2 $atom:monomers[11]/C1 - $bond:bb12 @bond:MonomerTypes/bb $atom:monomers[11]/C2 $atom:monomers[12]/C1 - $bond:bb13 @bond:MonomerTypes/bb $atom:monomers[12]/C2 $atom:monomers[13]/C1 - $bond:bb14 @bond:MonomerTypes/bb $atom:monomers[13]/C2 $atom:monomers[14]/C1 - $bond:bb15 @bond:MonomerTypes/bb $atom:monomers[14]/C2 $atom:monomers[15]/C1 - $bond:bb16 @bond:MonomerTypes/bb $atom:monomers[15]/C2 $atom:monomers[16]/C1 - $bond:bb17 @bond:MonomerTypes/bb $atom:monomers[16]/C2 $atom:monomers[17]/C1 - $bond:bb18 @bond:MonomerTypes/bb $atom:monomers[17]/C2 $atom:monomers[18]/C1 - $bond:bb19 @bond:MonomerTypes/bb $atom:monomers[18]/C2 $atom:monomers[19]/C1 - $bond:bb20 @bond:MonomerTypes/bb $atom:monomers[19]/C2 $atom:monomers[20]/C1 - $bond:bb21 @bond:MonomerTypes/bb $atom:monomers[20]/C2 $atom:monomers[21]/C1 - $bond:bb22 @bond:MonomerTypes/bb $atom:monomers[21]/C2 $atom:monomers[22]/C1 - $bond:bb23 @bond:MonomerTypes/bb $atom:monomers[22]/C2 $atom:monomers[23]/C1 - $bond:bb24 @bond:MonomerTypes/bb $atom:monomers[23]/C2 $atom:monomers[24]/C1 - $bond:bb25 @bond:MonomerTypes/bb $atom:monomers[24]/C2 $atom:monomers[25]/C1 - $bond:bb26 @bond:MonomerTypes/bb $atom:monomers[25]/C2 $atom:monomers[26]/C1 - $bond:bb27 @bond:MonomerTypes/bb $atom:monomers[26]/C2 $atom:monomers[27]/C1 - $bond:bb28 @bond:MonomerTypes/bb $atom:monomers[27]/C2 $atom:monomers[28]/C1 - $bond:bb29 @bond:MonomerTypes/bb $atom:monomers[28]/C2 $atom:monomers[29]/C1 - $bond:bb30 @bond:MonomerTypes/bb $atom:monomers[29]/C2 $atom:monomers[30]/C1 - $bond:bb31 @bond:MonomerTypes/bb $atom:monomers[30]/C2 $atom:monomers[31]/C1 - $bond:bb32 @bond:MonomerTypes/bb $atom:monomers[31]/C2 $atom:monomers[32]/C1 - $bond:bb33 @bond:MonomerTypes/bb $atom:monomers[32]/C2 $atom:monomers[33]/C1 - $bond:bb34 @bond:MonomerTypes/bb $atom:monomers[33]/C2 $atom:monomers[34]/C1 - $bond:bb35 @bond:MonomerTypes/bb $atom:monomers[34]/C2 $atom:monomers[35]/C1 - $bond:bb36 @bond:MonomerTypes/bb $atom:monomers[35]/C2 $atom:monomers[36]/C1 - $bond:bb37 @bond:MonomerTypes/bb $atom:monomers[36]/C2 $atom:monomers[37]/C1 - $bond:bb38 @bond:MonomerTypes/bb $atom:monomers[37]/C2 $atom:monomers[38]/C1 - $bond:bb39 @bond:MonomerTypes/bb $atom:monomers[38]/C2 $atom:monomers[39]/C1 - $bond:bb40 @bond:MonomerTypes/bb $atom:monomers[39]/C2 $atom:monomers[40]/C1 - $bond:bb41 @bond:MonomerTypes/bb $atom:monomers[40]/C2 $atom:monomers[41]/C1 - $bond:bb42 @bond:MonomerTypes/bb $atom:monomers[41]/C2 $atom:monomers[42]/C1 - $bond:bb43 @bond:MonomerTypes/bb $atom:monomers[42]/C2 $atom:monomers[43]/C1 - $bond:bb44 @bond:MonomerTypes/bb $atom:monomers[43]/C2 $atom:monomers[44]/C1 - $bond:bb45 @bond:MonomerTypes/bb $atom:monomers[44]/C2 $atom:monomers[45]/C1 - $bond:bb46 @bond:MonomerTypes/bb $atom:monomers[45]/C2 $atom:monomers[46]/C1 - $bond:bb47 @bond:MonomerTypes/bb $atom:monomers[46]/C2 $atom:monomers[47]/C1 - $bond:bb48 @bond:MonomerTypes/bb $atom:monomers[47]/C2 $atom:monomers[48]/C1 - $bond:bb49 @bond:MonomerTypes/bb $atom:monomers[48]/C2 $atom:monomers[49]/C1 - $bond:bb50 @bond:MonomerTypes/bb $atom:monomers[49]/C2 $atom:monomers[50]/C1 - $bond:bb51 @bond:MonomerTypes/bb $atom:monomers[50]/C2 $atom:monomers[51]/C1 - $bond:bb52 @bond:MonomerTypes/bb $atom:monomers[51]/C2 $atom:monomers[52]/C1 - $bond:bb53 @bond:MonomerTypes/bb $atom:monomers[52]/C2 $atom:monomers[53]/C1 - $bond:bb54 @bond:MonomerTypes/bb $atom:monomers[53]/C2 $atom:monomers[54]/C1 - $bond:bb55 @bond:MonomerTypes/bb $atom:monomers[54]/C2 $atom:monomers[55]/C1 - $bond:bb56 @bond:MonomerTypes/bb $atom:monomers[55]/C2 $atom:monomers[56]/C1 - $bond:bb57 @bond:MonomerTypes/bb $atom:monomers[56]/C2 $atom:monomers[57]/C1 - $bond:bb58 @bond:MonomerTypes/bb $atom:monomers[57]/C2 $atom:monomers[58]/C1 - $bond:bb59 @bond:MonomerTypes/bb $atom:monomers[58]/C2 $atom:monomers[59]/C1 - $bond:bb60 @bond:MonomerTypes/bb $atom:monomers[59]/C2 $atom:monomers[60]/C1 - $bond:bb61 @bond:MonomerTypes/bb $atom:monomers[60]/C2 $atom:monomers[61]/C1 - $bond:bb62 @bond:MonomerTypes/bb $atom:monomers[61]/C2 $atom:monomers[62]/C1 - $bond:bb63 @bond:MonomerTypes/bb $atom:monomers[62]/C2 $atom:monomers[63]/C1 - $bond:bb64 @bond:MonomerTypes/bb $atom:monomers[63]/C2 $atom:monomers[64]/C1 - $bond:bb65 @bond:MonomerTypes/bb $atom:monomers[64]/C2 $atom:monomers[65]/C1 - $bond:bb66 @bond:MonomerTypes/bb $atom:monomers[65]/C2 $atom:monomers[66]/C1 - $bond:bb67 @bond:MonomerTypes/bb $atom:monomers[66]/C2 $atom:monomers[67]/C1 - $bond:bb68 @bond:MonomerTypes/bb $atom:monomers[67]/C2 $atom:monomers[68]/C1 - $bond:bb69 @bond:MonomerTypes/bb $atom:monomers[68]/C2 $atom:monomers[69]/C1 - $bond:bb70 @bond:MonomerTypes/bb $atom:monomers[69]/C2 $atom:monomers[70]/C1 - $bond:bb71 @bond:MonomerTypes/bb $atom:monomers[70]/C2 $atom:monomers[71]/C1 - $bond:bb72 @bond:MonomerTypes/bb $atom:monomers[71]/C2 $atom:monomers[72]/C1 - $bond:bb73 @bond:MonomerTypes/bb $atom:monomers[72]/C2 $atom:monomers[73]/C1 - $bond:bb74 @bond:MonomerTypes/bb $atom:monomers[73]/C2 $atom:monomers[74]/C1 - $bond:bb75 @bond:MonomerTypes/bb $atom:monomers[74]/C2 $atom:monomers[75]/C1 - $bond:bb76 @bond:MonomerTypes/bb $atom:monomers[75]/C2 $atom:monomers[76]/C1 - $bond:bb77 @bond:MonomerTypes/bb $atom:monomers[76]/C2 $atom:monomers[77]/C1 - $bond:bb78 @bond:MonomerTypes/bb $atom:monomers[77]/C2 $atom:monomers[78]/C1 - $bond:bb79 @bond:MonomerTypes/bb $atom:monomers[78]/C2 $atom:monomers[79]/C1 - $bond:bb80 @bond:MonomerTypes/bb $atom:monomers[79]/C2 $atom:monomers[80]/C1 - $bond:bb81 @bond:MonomerTypes/bb $atom:monomers[80]/C2 $atom:monomers[81]/C1 - $bond:bb82 @bond:MonomerTypes/bb $atom:monomers[81]/C2 $atom:monomers[82]/C1 - $bond:bb83 @bond:MonomerTypes/bb $atom:monomers[82]/C2 $atom:monomers[83]/C1 - $bond:bb84 @bond:MonomerTypes/bb $atom:monomers[83]/C2 $atom:monomers[84]/C1 - $bond:bb85 @bond:MonomerTypes/bb $atom:monomers[84]/C2 $atom:monomers[85]/C1 - $bond:bb86 @bond:MonomerTypes/bb $atom:monomers[85]/C2 $atom:monomers[86]/C1 - $bond:bb87 @bond:MonomerTypes/bb $atom:monomers[86]/C2 $atom:monomers[87]/C1 - $bond:bb88 @bond:MonomerTypes/bb $atom:monomers[87]/C2 $atom:monomers[88]/C1 - $bond:bb89 @bond:MonomerTypes/bb $atom:monomers[88]/C2 $atom:monomers[89]/C1 - $bond:bb90 @bond:MonomerTypes/bb $atom:monomers[89]/C2 $atom:monomers[90]/C1 - $bond:bb91 @bond:MonomerTypes/bb $atom:monomers[90]/C2 $atom:monomers[91]/C1 - $bond:bb92 @bond:MonomerTypes/bb $atom:monomers[91]/C2 $atom:monomers[92]/C1 - $bond:bb93 @bond:MonomerTypes/bb $atom:monomers[92]/C2 $atom:monomers[93]/C1 - $bond:bb94 @bond:MonomerTypes/bb $atom:monomers[93]/C2 $atom:monomers[94]/C1 - $bond:bb95 @bond:MonomerTypes/bb $atom:monomers[94]/C2 $atom:monomers[95]/C1 - $bond:bb96 @bond:MonomerTypes/bb $atom:monomers[95]/C2 $atom:monomers[96]/C1 - $bond:bb97 @bond:MonomerTypes/bb $atom:monomers[96]/C2 $atom:monomers[97]/C1 - $bond:bb98 @bond:MonomerTypes/bb $atom:monomers[97]/C2 $atom:monomers[98]/C1 - $bond:bb99 @bond:MonomerTypes/bb $atom:monomers[98]/C2 $atom:monomers[99]/C1 - $bond:bb100 @bond:MonomerTypes/bb $atom:monomers[99]/C2 $atom:monomers[100]/C1 - $bond:bb101 @bond:MonomerTypes/bb $atom:monomers[100]/C2 $atom:monomers[101]/C1 - $bond:bb102 @bond:MonomerTypes/bb $atom:monomers[101]/C2 $atom:monomers[102]/C1 - $bond:bb103 @bond:MonomerTypes/bb $atom:monomers[102]/C2 $atom:monomers[103]/C1 - $bond:bb104 @bond:MonomerTypes/bb $atom:monomers[103]/C2 $atom:monomers[104]/C1 - $bond:bb105 @bond:MonomerTypes/bb $atom:monomers[104]/C2 $atom:monomers[105]/C1 - $bond:bb106 @bond:MonomerTypes/bb $atom:monomers[105]/C2 $atom:monomers[106]/C1 - $bond:bb107 @bond:MonomerTypes/bb $atom:monomers[106]/C2 $atom:monomers[107]/C1 - $bond:bb108 @bond:MonomerTypes/bb $atom:monomers[107]/C2 $atom:monomers[108]/C1 - $bond:bb109 @bond:MonomerTypes/bb $atom:monomers[108]/C2 $atom:monomers[109]/C1 - $bond:bb110 @bond:MonomerTypes/bb $atom:monomers[109]/C2 $atom:monomers[110]/C1 - $bond:bb111 @bond:MonomerTypes/bb $atom:monomers[110]/C2 $atom:monomers[111]/C1 - $bond:bb112 @bond:MonomerTypes/bb $atom:monomers[111]/C2 $atom:monomers[112]/C1 - $bond:bb113 @bond:MonomerTypes/bb $atom:monomers[112]/C2 $atom:monomers[113]/C1 - $bond:bb114 @bond:MonomerTypes/bb $atom:monomers[113]/C2 $atom:monomers[114]/C1 - $bond:bb115 @bond:MonomerTypes/bb $atom:monomers[114]/C2 $atom:monomers[115]/C1 - $bond:bb116 @bond:MonomerTypes/bb $atom:monomers[115]/C2 $atom:monomers[116]/C1 - $bond:bb117 @bond:MonomerTypes/bb $atom:monomers[116]/C2 $atom:monomers[117]/C1 - $bond:bb118 @bond:MonomerTypes/bb $atom:monomers[117]/C2 $atom:monomers[118]/C1 - $bond:bb119 @bond:MonomerTypes/bb $atom:monomers[118]/C2 $atom:monomers[119]/C1 - $bond:bb120 @bond:MonomerTypes/bb $atom:monomers[119]/C2 $atom:monomers[120]/C1 - $bond:bb121 @bond:MonomerTypes/bb $atom:monomers[120]/C2 $atom:monomers[121]/C1 - $bond:bb122 @bond:MonomerTypes/bb $atom:monomers[121]/C2 $atom:monomers[122]/C1 - $bond:bb123 @bond:MonomerTypes/bb $atom:monomers[122]/C2 $atom:monomers[123]/C1 - $bond:bb124 @bond:MonomerTypes/bb $atom:monomers[123]/C2 $atom:monomers[124]/C1 - $bond:bb125 @bond:MonomerTypes/bb $atom:monomers[124]/C2 $atom:monomers[125]/C1 - $bond:bb126 @bond:MonomerTypes/bb $atom:monomers[125]/C2 $atom:monomers[126]/C1 - $bond:bb127 @bond:MonomerTypes/bb $atom:monomers[126]/C2 $atom:monomers[127]/C1 - $bond:bb128 @bond:MonomerTypes/bb $atom:monomers[127]/C2 $atom:monomers[128]/C1 - $bond:bb129 @bond:MonomerTypes/bb $atom:monomers[128]/C2 $atom:monomers[129]/C1 - $bond:bb130 @bond:MonomerTypes/bb $atom:monomers[129]/C2 $atom:monomers[130]/C1 - $bond:bb131 @bond:MonomerTypes/bb $atom:monomers[130]/C2 $atom:monomers[131]/C1 - $bond:bb132 @bond:MonomerTypes/bb $atom:monomers[131]/C2 $atom:monomers[132]/C1 - $bond:bb133 @bond:MonomerTypes/bb $atom:monomers[132]/C2 $atom:monomers[133]/C1 - $bond:bb134 @bond:MonomerTypes/bb $atom:monomers[133]/C2 $atom:monomers[134]/C1 - $bond:bb135 @bond:MonomerTypes/bb $atom:monomers[134]/C2 $atom:monomers[135]/C1 - $bond:bb136 @bond:MonomerTypes/bb $atom:monomers[135]/C2 $atom:monomers[136]/C1 - $bond:bb137 @bond:MonomerTypes/bb $atom:monomers[136]/C2 $atom:monomers[137]/C1 - $bond:bb138 @bond:MonomerTypes/bb $atom:monomers[137]/C2 $atom:monomers[138]/C1 - $bond:bb139 @bond:MonomerTypes/bb $atom:monomers[138]/C2 $atom:monomers[139]/C1 - $bond:bb140 @bond:MonomerTypes/bb $atom:monomers[139]/C2 $atom:monomers[140]/C1 - $bond:bb141 @bond:MonomerTypes/bb $atom:monomers[140]/C2 $atom:monomers[141]/C1 - $bond:bb142 @bond:MonomerTypes/bb $atom:monomers[141]/C2 $atom:monomers[142]/C1 - $bond:bb143 @bond:MonomerTypes/bb $atom:monomers[142]/C2 $atom:monomers[143]/C1 - $bond:bb144 @bond:MonomerTypes/bb $atom:monomers[143]/C2 $atom:monomers[144]/C1 - $bond:bb145 @bond:MonomerTypes/bb $atom:monomers[144]/C2 $atom:monomers[145]/C1 - $bond:bb146 @bond:MonomerTypes/bb $atom:monomers[145]/C2 $atom:monomers[146]/C1 - $bond:bb147 @bond:MonomerTypes/bb $atom:monomers[146]/C2 $atom:monomers[147]/C1 - $bond:bb148 @bond:MonomerTypes/bb $atom:monomers[147]/C2 $atom:monomers[148]/C1 - $bond:bb149 @bond:MonomerTypes/bb $atom:monomers[148]/C2 $atom:monomers[149]/C1 - $bond:bb150 @bond:MonomerTypes/bb $atom:monomers[149]/C2 $atom:monomers[150]/C1 - $bond:bb151 @bond:MonomerTypes/bb $atom:monomers[150]/C2 $atom:monomers[151]/C1 - $bond:bb152 @bond:MonomerTypes/bb $atom:monomers[151]/C2 $atom:monomers[152]/C1 - $bond:bb153 @bond:MonomerTypes/bb $atom:monomers[152]/C2 $atom:monomers[153]/C1 - $bond:bb154 @bond:MonomerTypes/bb $atom:monomers[153]/C2 $atom:monomers[154]/C1 - $bond:bb155 @bond:MonomerTypes/bb $atom:monomers[154]/C2 $atom:monomers[155]/C1 - $bond:bb156 @bond:MonomerTypes/bb $atom:monomers[155]/C2 $atom:monomers[156]/C1 - $bond:bb157 @bond:MonomerTypes/bb $atom:monomers[156]/C2 $atom:monomers[157]/C1 - $bond:bb158 @bond:MonomerTypes/bb $atom:monomers[157]/C2 $atom:monomers[158]/C1 - $bond:bb159 @bond:MonomerTypes/bb $atom:monomers[158]/C2 $atom:monomers[159]/C1 - $bond:bb160 @bond:MonomerTypes/bb $atom:monomers[159]/C2 $atom:monomers[160]/C1 - $bond:bb161 @bond:MonomerTypes/bb $atom:monomers[160]/C2 $atom:monomers[161]/C1 - $bond:bb162 @bond:MonomerTypes/bb $atom:monomers[161]/C2 $atom:monomers[162]/C1 - $bond:bb163 @bond:MonomerTypes/bb $atom:monomers[162]/C2 $atom:monomers[163]/C1 - $bond:bb164 @bond:MonomerTypes/bb $atom:monomers[163]/C2 $atom:monomers[164]/C1 - $bond:bb165 @bond:MonomerTypes/bb $atom:monomers[164]/C2 $atom:monomers[165]/C1 - $bond:bb166 @bond:MonomerTypes/bb $atom:monomers[165]/C2 $atom:monomers[166]/C1 - $bond:bb167 @bond:MonomerTypes/bb $atom:monomers[166]/C2 $atom:monomers[167]/C1 - $bond:bb168 @bond:MonomerTypes/bb $atom:monomers[167]/C2 $atom:monomers[168]/C1 - $bond:bb169 @bond:MonomerTypes/bb $atom:monomers[168]/C2 $atom:monomers[169]/C1 - $bond:bb170 @bond:MonomerTypes/bb $atom:monomers[169]/C2 $atom:monomers[170]/C1 - $bond:bb171 @bond:MonomerTypes/bb $atom:monomers[170]/C2 $atom:monomers[171]/C1 - $bond:bb172 @bond:MonomerTypes/bb $atom:monomers[171]/C2 $atom:monomers[172]/C1 - $bond:bb173 @bond:MonomerTypes/bb $atom:monomers[172]/C2 $atom:monomers[173]/C1 - $bond:bb174 @bond:MonomerTypes/bb $atom:monomers[173]/C2 $atom:monomers[174]/C1 - $bond:bb175 @bond:MonomerTypes/bb $atom:monomers[174]/C2 $atom:monomers[175]/C1 - $bond:bb176 @bond:MonomerTypes/bb $atom:monomers[175]/C2 $atom:monomers[176]/C1 - $bond:bb177 @bond:MonomerTypes/bb $atom:monomers[176]/C2 $atom:monomers[177]/C1 - $bond:bb178 @bond:MonomerTypes/bb $atom:monomers[177]/C2 $atom:monomers[178]/C1 - $bond:bb179 @bond:MonomerTypes/bb $atom:monomers[178]/C2 $atom:monomers[179]/C1 - $bond:bb180 @bond:MonomerTypes/bb $atom:monomers[179]/C2 $atom:monomers[180]/C1 - $bond:bb181 @bond:MonomerTypes/bb $atom:monomers[180]/C2 $atom:monomers[181]/C1 - $bond:bb182 @bond:MonomerTypes/bb $atom:monomers[181]/C2 $atom:monomers[182]/C1 - $bond:bb183 @bond:MonomerTypes/bb $atom:monomers[182]/C2 $atom:monomers[183]/C1 - $bond:bb184 @bond:MonomerTypes/bb $atom:monomers[183]/C2 $atom:monomers[184]/C1 - $bond:bb185 @bond:MonomerTypes/bb $atom:monomers[184]/C2 $atom:monomers[185]/C1 - $bond:bb186 @bond:MonomerTypes/bb $atom:monomers[185]/C2 $atom:monomers[186]/C1 - $bond:bb187 @bond:MonomerTypes/bb $atom:monomers[186]/C2 $atom:monomers[187]/C1 - $bond:bb188 @bond:MonomerTypes/bb $atom:monomers[187]/C2 $atom:monomers[188]/C1 - $bond:bb189 @bond:MonomerTypes/bb $atom:monomers[188]/C2 $atom:monomers[189]/C1 - $bond:bb190 @bond:MonomerTypes/bb $atom:monomers[189]/C2 $atom:monomers[190]/C1 - $bond:bb191 @bond:MonomerTypes/bb $atom:monomers[190]/C2 $atom:monomers[191]/C1 - $bond:bb192 @bond:MonomerTypes/bb $atom:monomers[191]/C2 $atom:monomers[192]/C1 - $bond:bb193 @bond:MonomerTypes/bb $atom:monomers[192]/C2 $atom:monomers[193]/C1 - $bond:bb194 @bond:MonomerTypes/bb $atom:monomers[193]/C2 $atom:monomers[194]/C1 - $bond:bb195 @bond:MonomerTypes/bb $atom:monomers[194]/C2 $atom:monomers[195]/C1 - $bond:bb196 @bond:MonomerTypes/bb $atom:monomers[195]/C2 $atom:monomers[196]/C1 - $bond:bb197 @bond:MonomerTypes/bb $atom:monomers[196]/C2 $atom:monomers[197]/C1 - $bond:bb198 @bond:MonomerTypes/bb $atom:monomers[197]/C2 $atom:monomers[198]/C1 - $bond:bb199 @bond:MonomerTypes/bb $atom:monomers[198]/C2 $atom:monomers[199]/C1 - } - - - # These lines of moltemplate script above were generated in python: - # - # for i in range(0,199): - # print('$bond:bb'+str(i+1)+' @bond:MonomerTypes/bb $atom:monomers[' - # +str(i)+']/C2 $atom:monomers['+str(i+1)+']/C1') - - - # Finally, create a molecule ID number for this large polymer object - - create_var { $mol } - -} # Polymer200 - - - -# Angle, dihedral and improper interactions will be generated -# automatically according to the instructions in "monomer.lt" diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt deleted file mode 100644 index 7fced41437..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/moltemplate_files/system.lt +++ /dev/null @@ -1,44 +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") { - 0.0 840.0 xlo xhi - 0.0 840.0 ylo yhi - 0.0 840.0 zlo zhi -} - - -import "polymer.lt" - -# Create 150 long polymers - -polymers = new Polymer200.rot(4,0,1,1).move(-360, 0,-360) - [15].move(0, 56, 0).rot(96, 0,1,0) - [10].move(0, 0, 80) - - - - - -# If you only want one polymer, try this instead: -# polymer = new Polymer200 - diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt deleted file mode 100644 index 8d8b09afd5..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.npt +++ /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 1.0 -dump 1 all custom 2000 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 100 # time interval for printing out "thermo" data - -# ------------------- NPT ----------------------- - -fix fxlan all langevin 500.0 500.0 120 48279 -fix fxnph all nph iso 900.0 900.0 1000 - -# Temperature = 500 degrees, Pressure = 900 atm - -run 100000 diff --git a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt deleted file mode 100644 index e58a946751..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/heteropolymer_melt_attempt1/run.in.nvt +++ /dev/null @@ -1,31 +0,0 @@ -# -- Init Section -- - -include system.in.init - -# -- Atom Definition Section -- - -#read_data system.data -# (You must run the npt simulation first.) -read_restart system_after_npt.rst - -# -- Settings Section -- - -include system.in.settings - -# -- Run Section -- - - -timestep 2.0 -dump 1 all custom 2000 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 - -fix 1 all nvt temp 500.0 500.0 100.0 - -# Temperature = 500 degrees - -run 100000 - -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 85bb1278f1..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_run.sh +++ /dev/null @@ -1,25 +0,0 @@ -# This is just an example. -# -# Note: The 3 files "run.in.min", "run.in.npt", and "run.in.nvt" are LAMMPS -# input scripts which link to the input scripts and data files you -# created earlier with moltemplate.sh: -# 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.npt # equilibrate the pressure -#"$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL) - -# 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.npt # equilibrate the pressure -#mpirun -np $NUMPROCS "$LAMMPS_COMMAND" -i run.in.nvt # production run (OPTIONAL) - 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_visualise.txt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualise.txt deleted file mode 100644 index 019afc1444..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/README_visualise.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 - 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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 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 7ed9567d45..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 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 all 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 a0f4d5a969..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/moltemplate_files/system.lt +++ /dev/null @@ -1,53 +0,0 @@ -import "ions.lt" # <- This defines the ions "NaIon" and "ClIon". - -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). - - -# 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, 0.01) - [10].move(3.45, 0.01, 0.01) - -# 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(5,5,5) -cl[*][*][*].move(12,12,12) - -# (The (5,5,5) and (12,12,12) 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.min b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.min deleted file mode 100644 index 992bcd22e6..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.min +++ /dev/null @@ -1,26 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - -dump 1 all custom 20 traj_min.lammpstrj id mol type x y z ix iy iz - -# fSHAKE was defined in system.in.settings. It is incompatible with "minimize". -unfix fSHAKE -minimize 1.0e-5 1.0e-7 100000 400000 - -# (For a system with ~6000 atoms, this takes 1-4 minutes on a i7 720 processor.) -# Alternate (faster) minimizer settings (about 10 sec): -# minimize 1.0e-4 1.0e-6 500 2000 - - -write_restart system_after_min.rst 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 dff24722bd..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt +++ /dev/null @@ -1,28 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -# I probably should minimize the system first, -# but it turns out to not be necessary in this case. -# Instead I just read the raw atom coordinates generated by moltemplate. -read_data system.data - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -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 50000 - -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 c42223a162..0000000000 --- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt +++ /dev/null @@ -1,33 +0,0 @@ -# ------------------------------- Initialization Section -------------------- - -include system.in.init - -# ------------------------------- Atom Definition Section ------------------- - -#read_data system.data -#read_restart system_after_min.rst -read_restart system_after_npt.rst - -# ------------------------------- Settings Section -------------------------- - -include system.in.settings - -# ------------------------------- Run Section ------------------------------- - - -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 1000000 - -write_restart system_after_nvt.rst - - diff --git a/tools/moltemplate/src/extract_lammps_data.py b/tools/moltemplate/src/extract_lammps_data.py deleted file mode 100755 index 59af89ca15..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 ExtractDataSection(f, - section_header, - comment_char = '#', - include_header = False, - return_line_nums = False): - inside_section = False - nonblank_encountered = False - i = 0 - for line_orig in f: - return_this_line = False - line = line_orig.strip() - if line == section_header: - inside_section = True - nonblank_encountered = False - if include_header: - return_this_line = True - # A block of blank lines (which dont immediately follow - # the section header-name) signal the end of a section: - elif len(line) == 0: - if inside_section and include_header: - 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 - - -def FindDataSection(f, - section_header, - comment_char = '#'): - i_section_start = -1 - i_section_stop = -1 - inside_section = False - nonblank_encountered = False - i = 0 - for line_orig in f: - line = line_orig.strip() - if line == section_header: - inside_section = True - nonblank_encountered = False - # A block of blank lines (which dont immediately follow - # the section header-name) signal the end of a section: - elif len(line) == 0: - if nonblank_encountered: - inside_section = False - i_section_stop = i - break - elif line[0] != comment_char: - if inside_section: - if not nonblank_encountered: - i_section_start = i # <- first non-blank line - nonblank_encountered = True - i += 1 - - if i_section_stop == -1: - if i_section_start != -1: - i_section_stop = i - - return (i_section_start, i_section_stop) - - -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_header=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 9ded475611..0000000000 --- a/tools/moltemplate/src/ltemplify.py +++ /dev/null @@ -1,1920 +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) - 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 = 'lemplify.py' - g_version_str = '0.2' - g_date_str = '2012-4-12' - sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n') - - 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', - 'special_bonds'])): - 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') - - 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] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_bonds.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS BONDS\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,2): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected are bonded\n' - ' to other atoms you didn\'t select.\n' - ' Are you sure you selected the correct atoms?\n') - - - - elif (line.strip() == 'Angles'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line == '': - break - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 5): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Angles section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$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] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_angles.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS ANGLES\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,3): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 3-body \"Angle\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - - - elif (line.strip() == 'Dihedrals'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Dihedrals section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$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] = '$atom:id'+tokens[2+n] - some_in_selection = True - else: - in_selections = False - if in_selections: - l_data_dihedrals.append((' '*indent)+(' '.join(tokens)+'\n')) - elif some_in_selection: - sys.stderr.write('WARNING: SELECTION BREAKS DIHEDRALS\n') - sys.stderr.write(' (between atom ids: ') - for n in range(0,4): - sys.stderr.write(str(atomids[n])+' ') - sys.stderr.write(')\n' - ' The atoms you selected participate in 4-body \"Dihedral\"\n' - ' interactions with other atoms you didn\'t select.\n' - ' (They will be ignored.)\n' - ' Are you sure you selected the correct atoms?\n') - - - elif (line.strip() == 'Impropers'): - sys.stderr.write(' processing \"'+line.strip()+'\"\n') - while lex: - line = lex.ReadLine() - if line.strip() in data_file_header_names: - lex.push_raw_text(line) # <- Save line for later - break - tokens = line.strip().split() - if len(tokens) > 0: - if (len(tokens) < 6): - raise InputError('Error: near or before '+ErrorLeader(infile, lineno)+'\n' - ' Nonsensical line in Impropers section:\n' - ' \"'+line.strip()+'\"\n') - #tokens[0] = '$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') - - - 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 discourages 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[0] = '@bond:type'+tokens[0] - 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 and 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 and 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 and 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 and 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]) - else: - tokens[1] = i_str - tokens[2] = j_str - 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 and 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 and 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]) - else: - tokens[1] = i_str - 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:type'+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_final)+'}*@{bond:type'+str(j_b_final)+'}' - - if ((i_a in needed_bondtypes) and - (i_b in needed_bondtypes)): - 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_final)+'}*@{angle:type'+str(j_b_final)+'}' - - if ((i_a in needed_angletypes) and - (i_b in needed_angletypes)): - 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_final)+'}*@{dihedral:type'+str(j_b_final)+'}' - - if ((i_a in needed_dihedraltypes) and - (i_b in needed_dihedraltypes)): - 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_final)+'}*@{improper:type'+str(j_b_final)+'}' - - if ((i_a in needed_impropertypes) and - (i_b in needed_impropertypes)): - 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') - - #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_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)) - 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)) - 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)) - 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)) - 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)) - 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)) - - # 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - - # 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)) - 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)) - 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)) - - 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)) - else: - sys.stderr.write('Warning: missing \"Atoms\" section.\n' - ' (Did you include a LAMMPS data file in your argument list?)\n') - - # 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - 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)) - - if len(l_in_settings) > 0: - 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)) - if len(l_in_init) > 0: - 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 mol_name != '': - sys.stdout.write('\n} # end of \"'+mol_name+'\" type definition\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 f1bf96cc4f..0000000000 --- a/tools/moltemplate/src/lttree.py +++ /dev/null @@ -1,729 +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. - -""" -ltree_count.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 - -data_atoms = 'Data Atoms' # <-- The name of the file/section storing Atom data. - - - -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 - - - - -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: '+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') - 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('+__file__+'):\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('+__file__+'):\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' - #'## 5) Include a ##\n' - #'## write(\"Init.txt\"){atom_style ...} ##\n' - #'## statement in your .ttree file. ##\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 = lines[i] - 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