git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12922 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -1,70 +0,0 @@
|
||||
This example shows how to put a protein (inclusion) in a
|
||||
lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
|
||||
The DPPC lipid model is described here:
|
||||
G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
Physical Review E, Vol 72, 011915 (2005)
|
||||
(The DLPC model is a truncated version of DPPC. Modifications discussed below.)
|
||||
The protein model is described here:
|
||||
G. Bellesia, AI Jewett, and J-E Shea,
|
||||
Protein Science, Vol19 141-154 (2010)
|
||||
|
||||
--- PREREQUISITES: ---
|
||||
|
||||
1) This example requires the "dihedral_style fourier", which is currently
|
||||
in the USER-MISC package. Build LAMMPS with this package enabled using
|
||||
make yes-user-misc
|
||||
before compiling LAMMPS.
|
||||
(See http://lammps.sandia.gov/doc/Section_start.html#start_3 for details.)
|
||||
|
||||
2) This example may require additional features to be added to LAMMPS.
|
||||
If LAMMPS complains about an "Invalid pair_style", then
|
||||
a) download the "additional_lammps_code" from
|
||||
http://moltemplate.org (upper-left corner menu)
|
||||
b) unpack it
|
||||
c) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
d) (re)compile LAMMPS.
|
||||
|
||||
|
||||
----- Details --------
|
||||
|
||||
This example contains a coarse-grained model of a 4-helix bundle protein
|
||||
inserted into a lipid bilayer (made from a mixture of DPPC and DLPC).
|
||||
|
||||
-- Protein Model: --
|
||||
|
||||
The coarse-grained protein is described in:
|
||||
G. Bellesia, AI Jewett, and J-E Shea, Protein Science, Vol19 141-154 (2010)
|
||||
Here we use the "AUF2" model described in that paper.
|
||||
(The hydrophobic beads face outwards.)
|
||||
|
||||
-- Memebrane Model: --
|
||||
|
||||
The DPPC lipid bilayer described in:
|
||||
G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
Physical Review E, Vol 72, 011915 (2005)
|
||||
and:
|
||||
M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
J. Chem. Phys. 135, 244701 (2011)
|
||||
|
||||
As in Watson(JCP 2011), rigid bond-length constraints
|
||||
have been replaced by harmonic bonds.
|
||||
|
||||
A truncated version of this lipid (named "DLPC") has also been added.
|
||||
The bending stiffness of each lipid has been increased to compensate
|
||||
for the additional disorder resulting from mixing two different types
|
||||
of lipids together. (Otherwise pores appear.)
|
||||
Unlike the original "DPPC" molecule model, the new "DPPC" and "DLPC" models
|
||||
have not been carefully parameterized to reproduce the correct behavior in
|
||||
a lipid bilayer mixture.
|
||||
|
||||
|
||||
-------------
|
||||
|
||||
Instructions on how to build LAMMPS input files and
|
||||
run a short simulation are provided in other README files.
|
||||
|
||||
step 1)
|
||||
README_setup.sh
|
||||
|
||||
step2)
|
||||
README_run.sh
|
||||
@ -1,33 +0,0 @@
|
||||
# --- Running LAMMPS ---
|
||||
# -- Prerequisites: --
|
||||
# The "run.in.nvt" file is a LAMMPS input script containing
|
||||
# references to the input scripts and data files
|
||||
# you hopefully have created earlier with moltemplate.sh:
|
||||
# system.in.init, system.in.settings, system.data, and table_int.dat
|
||||
# If not, carry out the instructions in "README_setup.sh".
|
||||
#
|
||||
# -- Instructions: --
|
||||
# If "lmp_linux" is the name of the command you use to invoke lammps,
|
||||
# then you would run lammps on these files this way:
|
||||
|
||||
|
||||
lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension)
|
||||
|
||||
#or
|
||||
|
||||
lmp_linux -i run.in.nvt # Run a simulation at constant volume
|
||||
|
||||
#(Note: The constant volume simulation lacks pressure equilibration. These are
|
||||
# completely separate simulations. The results of the constant pressure
|
||||
# simulation are ignored when beginning the simulation at constant volume.
|
||||
# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# If you have compiled the MPI version of lammps, you can run lammps in parallel
|
||||
#mpirun -np 4 lmp_linux -i run.in.npt
|
||||
#or
|
||||
#mpirun -np 4 lmp_linux -i run.in.nvt
|
||||
# (assuming you have 4 processors available)
|
||||
@ -1,28 +0,0 @@
|
||||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# The "table_int.dat" file contains tabular data for the lipid INT-INT atom
|
||||
# 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
|
||||
# so I might look for a way to get rid of it later.)
|
||||
cp -f table_int.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
@ -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.)
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 83 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 69 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 50 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 66 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 69 KiB |
@ -1,254 +0,0 @@
|
||||
# This file defines a 4-helix bundle coarse-grained protein model (AUF2) used in
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
#
|
||||
# Strategy:
|
||||
#
|
||||
#1) First I'll define some building blocks (A16, B16, T3)
|
||||
# which are helices, sheets and turns of a predetermined length)
|
||||
#
|
||||
#2) Then I'll copy and paste them together to build
|
||||
# a 4-helix bundle (or a 4-strand beta-barrel).
|
||||
# This approach is optional. If your protein has helices which are not
|
||||
# identical, you should probably just include all 4 helices in a single
|
||||
# "Data Atoms" section and don't try to subdivide the protein into pieces.)
|
||||
|
||||
|
||||
|
||||
1beadProtSci2010 { # <-- enclose definitions in a namespace for portability
|
||||
|
||||
# A16 is a coarse-grained alpha-helix containing 16 residues (one "atom" each)
|
||||
|
||||
A16 {
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../sL 0.0 -2.4 -2.4 0.0
|
||||
$atom:a2 $mol:... @atom:../sL 0.0 2.4 -2.4 3.6
|
||||
$atom:a3 $mol:... @atom:../sH 0.0 2.4 2.4 7.2
|
||||
$atom:a4 $mol:... @atom:../sH 0.0 -2.4 2.4 10.8
|
||||
$atom:a5 $mol:... @atom:../sL 0.0 -2.4 -2.4 14.4
|
||||
$atom:a6 $mol:... @atom:../sL 0.0 2.4 -2.4 18.0
|
||||
$atom:a7 $mol:... @atom:../sH 0.0 2.4 2.4 21.6
|
||||
$atom:a8 $mol:... @atom:../sH 0.0 -2.4 2.4 25.2
|
||||
$atom:a9 $mol:... @atom:../sL 0.0 -2.4 -2.4 28.8
|
||||
$atom:a10 $mol:... @atom:../sL 0.0 2.4 -2.4 32.4
|
||||
$atom:a11 $mol:... @atom:../sH 0.0 2.4 2.4 36.0
|
||||
$atom:a12 $mol:... @atom:../sH 0.0 -2.4 2.4 39.6
|
||||
$atom:a13 $mol:... @atom:../sL 0.0 -2.4 -2.4 43.2
|
||||
$atom:a14 $mol:... @atom:../sL 0.0 2.4 -2.4 46.8
|
||||
$atom:a15 $mol:... @atom:../sH 0.0 2.4 2.4 50.4
|
||||
$atom:a16 $mol:... @atom:../sH 0.0 -2.4 2.4 54.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
|
||||
}
|
||||
|
||||
} # A16
|
||||
|
||||
|
||||
T3 { # T3 is a "turn" region consisting of 3 beads
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../tN 0.0 -4.8 0.0 0.0
|
||||
$atom:a2 $mol:... @atom:../tN 0.0 0.0 3.3 -1.44
|
||||
$atom:a3 $mol:... @atom:../tN 0.0 4.8 0.0 0.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
}
|
||||
|
||||
} # T3
|
||||
|
||||
|
||||
# ----- Now build a larger molecule using A16 and T3 -------
|
||||
|
||||
# Create a 4-Helix bundle.
|
||||
# In this version, the hydrophobic beads are poing outward.
|
||||
# I oriented them this way because I want to place this protein in a membrane.
|
||||
# (There is another file in this directory containing alternate version
|
||||
# of this same molecule with the hydrophobic beads pointing inward.)
|
||||
|
||||
4HelixInsideOut {
|
||||
helix1 = new A16.rot(-225, 0,0,1).move(-5.70,-5.70,-32.4)
|
||||
helix2 = new A16.rot(-135, 0,0,1).move( 5.70,-5.70,-28.8)
|
||||
helix3 = new A16.rot( -45, 0,0,1).move( 5.70, 5.70,-25.2)
|
||||
helix4 = new A16.rot( 45, 0,0,1).move(-5.70, 5.70,-21.6)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot( 10,0,0,1).move(0.78,-4.2, 27.9)
|
||||
turn2 = new T3.rot(-10,1,0,0).rot( 20,0,1,0).rot(-70,0,0,1).move(4.55, 2.4,-33.0)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(-20,0,1,0).rot(190,0,0,1).move(-0.78,4.2, 34.2)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixInsideOut
|
||||
|
||||
|
||||
# -------- Minor coordinates adjustment: -----------
|
||||
|
||||
# Those coordinates in the commands above are a little too large.
|
||||
# To make it easier to type them in, I was using sigma=6.0 Angstroms.
|
||||
# Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667)
|
||||
|
||||
4HelixInsideOut.scale(0.9166666666666666)
|
||||
|
||||
# Note: "scale()" only effects the initial coordinates of
|
||||
# the molecule, not the force field parameters.
|
||||
# (If you plan to minimize the molecule, you don't need to
|
||||
# be so careful about the initial coordinates. In that case,
|
||||
# you don't have worry about "scale()". Feel free to remove.)
|
||||
|
||||
|
||||
|
||||
# -------------- Force-Field Parameters ------------
|
||||
|
||||
# Units and force-field styles for this protein model
|
||||
# (These can be overridden later.)
|
||||
|
||||
write_once("In Init") {
|
||||
units real
|
||||
atom_style full
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid harmonic
|
||||
dihedral_style hybrid fourier
|
||||
pair_style hybrid lj/charmm/coul/charmm/inter es4k4l maxmax 21.0 24.0
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 #(turn on "1-4" interactions)
|
||||
}
|
||||
|
||||
# --- Distance Units ---
|
||||
# In this version of the model, sigma (the bond-length
|
||||
# and particle diameter) is rounded to 5.5 Angstroms.
|
||||
#
|
||||
# --- Energy & Temperature Units ---
|
||||
# In this protein model, "epsilon" represents the free energy
|
||||
# bonus for bringing two hydrophobic amino acids together.
|
||||
# Here I choose to set epsilon to 1.806551818181818 kCal/mole.
|
||||
# This value was chosen so that a temperature of 300 Kelvin lies at
|
||||
# 0.33 epsilon, which is the unfolding temperature of the marginally stable
|
||||
# "ASF1" protein model from the Bellesia et al 2010 paper.
|
||||
# This choice insures that both the "ASF1" model from that paper,
|
||||
# as well as the much more stable "AUF2" protein we use here (which
|
||||
# unfolds at 0.42*eps) should definitely remain stable at 300 degrees Kelvin,
|
||||
# in the bulk at least. (However it's not clear that these energy
|
||||
# parameters will work well for a protein in membrane. Perhaps I'll
|
||||
# run some tests and fine tune these parameters for this scenario.)
|
||||
|
||||
|
||||
# 2-body (non-bonded) interactions:
|
||||
#
|
||||
# Uij(r) = 4*eps_ij * (K*(sig_ij/r)^12 + L*(sig_ij/r)^6)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
#
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:sH @atom:sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
pair_coeff @atom:sL @atom:sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
pair_coeff @atom:tN @atom:tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
}
|
||||
|
||||
# The exact value of the bond_coeff does not matter too much as long as
|
||||
# it is "stiff enough". Here I use a softer bond spring than the one
|
||||
# used in the paper so that I can increase the time step.
|
||||
# I also use a relatively soft spring to constrain the bond angles.
|
||||
|
||||
# bond_coeff bondType bondstylename k r0
|
||||
|
||||
write_once("In Settings") {
|
||||
bond_coeff @bond:1beadProtSci2010/backbone harmonic 10.0 5.5
|
||||
}
|
||||
|
||||
|
||||
|
||||
# We use the same bond-angle forces whenever
|
||||
# there are 3 consecutively-bonded atoms:
|
||||
#
|
||||
# angleType atomtypes1 2 3 bondtypes1 2
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:* @bond:*
|
||||
}
|
||||
|
||||
# angle_coeff angleType anglestylename k theta0
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone harmonic 100.0 105.0
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
# Dihedral interactions are also determined by atom-type name in this case.
|
||||
# I chose atoms whose type-names begin with "t" to be "turn" atoms.
|
||||
# Atoms whose type-names begin with "s" could be either helices or sheets.
|
||||
# (In this case, helices. In this example, we use the @dihedral:delta65_0
|
||||
# parameters. This corresponds to the "AUF2" model from the
|
||||
# Bellesia et. al 2010 paper.)
|
||||
|
||||
# dihedralType atomtypes1 2 3 4 bondtypes1 2 3
|
||||
|
||||
write_once("Data Dihedrals By Type") {
|
||||
@dihedral:delta65_0 @atom:s* @atom:s* @atom:s* @atom:s* * * *
|
||||
|
||||
# If "tN" (turn) atoms are present, use the @dihedral:turn parameters
|
||||
|
||||
@dihedral:turn @atom:tN @atom:* @atom:* @atom:* * * *
|
||||
}
|
||||
|
||||
|
||||
# From the Bellesia et al 2010 paper:
|
||||
# for helices: U_{dih}(\phi) = 1.2*(cos(3\phi) + cos(\phi+\delta))
|
||||
# for turns: U_{dih}(\phi) = 0.2*cos(3\phi)
|
||||
#
|
||||
# General formula used for "dihedral_style fourier":
|
||||
# U_{dih}(\phi) = \Sum_{i=1}^m K_i [ 1.0 + cos(n_i \phi - d_i) ]
|
||||
#
|
||||
# Syntax:
|
||||
# dihedralType dihedralstyle m K_1 n_1 d_1 K2 n_2 d_2 ...
|
||||
|
||||
write_once("In Settings") {
|
||||
dihedral_coeff @dihedral:delta60_0 fourier 2 2.167862 3 0 2.167862 1 -60.0
|
||||
dihedral_coeff @dihedral:delta62_5 fourier 2 2.167862 3 0 2.167862 1 -62.5
|
||||
dihedral_coeff @dihedral:delta65_0 fourier 2 2.167862 3 0 2.167862 1 -65.0
|
||||
dihedral_coeff @dihedral:turn fourier 1 0.361310 3 0
|
||||
# Note: 2.167862=1.2*epsilon and 0.361310=0.2*epsilon.
|
||||
}
|
||||
|
||||
|
||||
# --- Mass Units ---
|
||||
# Typical amino acids weigh approximately 110.0 grams/mole. (Rounding down):
|
||||
write_once("Data Masses") {
|
||||
@atom:1beadProtSci2010/sH 100.0
|
||||
@atom:1beadProtSci2010/sL 100.0
|
||||
@atom:1beadProtSci2010/tN 100.0
|
||||
}
|
||||
|
||||
} # 1beadProtSci2010 (namespace)
|
||||
|
||||
@ -1,225 +0,0 @@
|
||||
### THIS FILE IS OPTIONAL AND IS NOT NECESSARY. IN THIS FILE, I DEFINED SOME ##
|
||||
### ADDITIONAL PROTEIN TYPES FROM THE PAPER THAT I DID NOT USE IN THIS EXAMPLE##
|
||||
#
|
||||
# This file defines a family of coarse-grained protein models used in:
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
#
|
||||
# Strategy:
|
||||
#
|
||||
#1) First I'll define some building blocks (A16, B16, T3)
|
||||
# which are helices, sheets and turns of a predetermined length)
|
||||
|
||||
import "1beadProtSci2010.lt"
|
||||
|
||||
# We defined A16 and T3 earlier in "1beadPRotSci2010.lt" Will define B16 below
|
||||
#
|
||||
#2) Then I'll copy and paste them together to build
|
||||
# a 4-helix bundle or a 4-strand beta-barrel.
|
||||
|
||||
|
||||
1beadProtSci2010 { #<-- Add new molecules to existing namespace defined earlier
|
||||
# This way we don't have to start from scratch. We can
|
||||
# use all the atom types and angle settings defined earlier
|
||||
|
||||
# B16 is a coarse-grained beta-strand containing 16 residues (one "atom" each)
|
||||
|
||||
B16 {
|
||||
|
||||
# AtomID MoleculeID AtomType Charge X Y Z
|
||||
|
||||
write('Data Atoms') {
|
||||
$atom:a1 $mol:... @atom:../sL 0.0 -1.8 0.0 0.0
|
||||
$atom:a2 $mol:... @atom:../sH 0.0 1.8 0.0 4.8
|
||||
$atom:a3 $mol:... @atom:../sL 0.0 -1.8 0.0 9.6
|
||||
$atom:a4 $mol:... @atom:../sH 0.0 1.8 0.0 14.4
|
||||
$atom:a5 $mol:... @atom:../sL 0.0 -1.8 0.0 19.2
|
||||
$atom:a6 $mol:... @atom:../sH 0.0 1.8 0.0 24.0
|
||||
$atom:a7 $mol:... @atom:../sL 0.0 -1.8 0.0 28.8
|
||||
$atom:a8 $mol:... @atom:../sH 0.0 1.8 0.0 33.6
|
||||
$atom:a9 $mol:... @atom:../sL 0.0 -1.8 0.0 38.4
|
||||
$atom:a10 $mol:... @atom:../sH 0.0 1.8 0.0 43.2
|
||||
$atom:a11 $mol:... @atom:../sL 0.0 -1.8 0.0 48.0
|
||||
$atom:a12 $mol:... @atom:../sH 0.0 1.8 0.0 52.8
|
||||
$atom:a13 $mol:... @atom:../sL 0.0 -1.8 0.0 57.6
|
||||
$atom:a14 $mol:... @atom:../sH 0.0 1.8 0.0 62.4
|
||||
$atom:a15 $mol:... @atom:../sL 0.0 -1.8 0.0 67.2
|
||||
$atom:a16 $mol:... @atom:../sH 0.0 1.8 0.0 72.0
|
||||
}
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:b1 @bond:../backbone $atom:a1 $atom:a2
|
||||
$bond:b2 @bond:../backbone $atom:a2 $atom:a3
|
||||
$bond:b3 @bond:../backbone $atom:a3 $atom:a4
|
||||
$bond:b4 @bond:../backbone $atom:a4 $atom:a5
|
||||
$bond:b5 @bond:../backbone $atom:a5 $atom:a6
|
||||
$bond:b6 @bond:../backbone $atom:a6 $atom:a7
|
||||
$bond:b7 @bond:../backbone $atom:a7 $atom:a8
|
||||
$bond:b8 @bond:../backbone $atom:a8 $atom:a9
|
||||
$bond:b9 @bond:../backbone $atom:a9 $atom:a10
|
||||
$bond:b10 @bond:../backbone $atom:a10 $atom:a11
|
||||
$bond:b11 @bond:../backbone $atom:a11 $atom:a12
|
||||
$bond:b12 @bond:../backbone $atom:a12 $atom:a13
|
||||
$bond:b13 @bond:../backbone $atom:a13 $atom:a14
|
||||
$bond:b14 @bond:../backbone $atom:a14 $atom:a15
|
||||
$bond:b15 @bond:../backbone $atom:a15 $atom:a16
|
||||
}
|
||||
|
||||
} # B16
|
||||
|
||||
# ----- Now build larger molecules using B16 and T3 -------
|
||||
|
||||
|
||||
4SheetBarrel {
|
||||
sheet1 = new B16.rot( 45, 0,0,1).move(-4.762203156,-4.762203156, -36.0)
|
||||
sheet2 = new B16.rot( 135, 0,0,1).move( 4.762203156,-4.762203156, -36.0)
|
||||
sheet3 = new B16.rot( 225, 0,0,1).move( 4.762203156, 4.762203156, -36.0)
|
||||
sheet4 = new B16.rot( 315, 0,0,1).move(-4.762203156, 4.762203156, -36.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 0, 0,0,1).move( 0, -7.8, 39.6)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(-90,0,0,1).move(4.2, 0.0,-41.4)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(-180,0,0,1).move( 0, 7.8, 39.6)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:sheet1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:sheet2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:sheet3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:sheet2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:sheet3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:sheet4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
}
|
||||
|
||||
|
||||
# Below I define several alternate conformations of the"4HelixBundleInsideOut"
|
||||
# molecule I defined earlier in "1beadProtSci2010.lt". Same molecule however.
|
||||
|
||||
4HelixBundle {
|
||||
helix1 = new A16.rot( -45, 0,0,1).move(-5.70,-5.70,-32.4)
|
||||
helix2 = new A16.rot( 45, 0,0,1).move( 5.70,-5.70,-28.8)
|
||||
helix3 = new A16.rot( 135, 0,0,1).move( 5.70, 5.70,-25.2)
|
||||
helix4 = new A16.rot( 225, 0,0,1).move(-5.70, 5.70,-21.6)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
|
||||
turn1 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot( 8,0,0,1).move(-3.6,-4.8,28.2)
|
||||
turn2 = new T3.rot(-5,1,0,0).rot( 21,0,1,0).rot(-100,0,0,1).move(4.2,-0.66,-30.9)
|
||||
turn3 = new T3.rot(150,1,0,0).rot(-23,0,1,0).rot(188,0,0,1).move(3.6,4.8,35.4)
|
||||
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixBundle
|
||||
|
||||
|
||||
|
||||
|
||||
# --- alternate conformations (same molecule) ----
|
||||
|
||||
# In the following version, the helices are oriented in a similar way,
|
||||
# but they are separated a little further away from eachother.
|
||||
|
||||
4HelixBundleLoose {
|
||||
|
||||
helix1 = new A16.rot( -45, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
|
||||
helix2 = new A16.rot( 45, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
|
||||
helix3 = new A16.rot( 135, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
|
||||
helix4 = new A16.rot( 225, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot(-17,0,0,1).move(-1.2,-4.2,32.4)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(-100,0,0,1).move(4.2,-0.9,-28.8)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(163,0,0,1).move(1.2,4.2,32.4)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
}
|
||||
|
||||
|
||||
# In following version, the helices are oriented in a similar way,
|
||||
# but they are separated a little further away from eachother.
|
||||
|
||||
4HelixInsideOutLoose {
|
||||
helix1 = new A16.rot(-225, 0,0,1).move(-6.7347723,-6.7347723, -27.0)
|
||||
helix2 = new A16.rot(-135, 0,0,1).move( 6.7347723,-6.7347723, -27.0)
|
||||
helix3 = new A16.rot( -45, 0,0,1).move( 6.7347723, 6.7347723, -27.0)
|
||||
helix4 = new A16.rot( 45, 0,0,1).move(-6.7347723, 6.7347723, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 10,0,0,1).move( 0.78,-4.2,28.8)
|
||||
turn2 = new T3.rot( 70,1,0,0).rot(-70,0,0,1).move( 10.8,2.4,-28.2)
|
||||
turn3 = new T3.rot(180,1,0,0).rot(190,0,0,1).move(-0.78,4.2,28.8)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixInsideOutLoose
|
||||
|
||||
|
||||
|
||||
|
||||
# In the following version, the 4 helices are arranged next to each other,
|
||||
# side-by-side, in a planar conformation (instead of a compact bundle).
|
||||
|
||||
4HelixPlanar {
|
||||
helix1 = new A16.rot(-00, 0,0,1).move(0, 0, -27.0)
|
||||
helix2 = new A16.rot( 00, 0,0,1).move(14.4, 0, -27.0)
|
||||
helix3 = new A16.rot(-00, 0,0,1).move(28.8, 0, -27.0)
|
||||
helix4 = new A16.rot( 00, 0,0,1).move(43.2, 0, -27.0)
|
||||
|
||||
turn1 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move( 4.8, 0, 31.8)
|
||||
turn2 = new T3.rot( 0,1,0,0).rot(180,0,0,1).move(19.2, 0,-31.8)
|
||||
turn3 = new T3.rot(180,1,0,0).rot( 0,0,0,1).move(34.6, 0, 31.8)
|
||||
|
||||
write('Data Bonds') {
|
||||
$bond:turn1a @bond:../backbone $atom:turn1/a1 $atom:helix1/a16
|
||||
$bond:turn1b @bond:../backbone $atom:turn1/a3 $atom:helix2/a16
|
||||
$bond:turn2a @bond:../backbone $atom:turn2/a1 $atom:helix3/a1
|
||||
$bond:turn2b @bond:../backbone $atom:turn2/a3 $atom:helix2/a1
|
||||
$bond:turn3a @bond:../backbone $atom:turn3/a1 $atom:helix3/a16
|
||||
$bond:turn3b @bond:../backbone $atom:turn3/a3 $atom:helix4/a16
|
||||
}
|
||||
create_var { $mol } # molecule ID number shared by all atoms in this protein
|
||||
|
||||
} # 4HelixPlanar
|
||||
|
||||
|
||||
# -------- Minor coordinates adjustment: -----------
|
||||
# Those coordinates in the commands above are a little too large.
|
||||
# To make it easier to type them in, I was using sigma=6.0 Angstroms.
|
||||
# Instead, here I'll try using sigma=5.5 Angstroms. 5.5/6 = 0.916667)
|
||||
|
||||
4SheetBarrel.scale(0.9166666666666666)
|
||||
4HelixBundle.scale(0.9166666666666666)
|
||||
4HelixBundleLoose.scale(0.9166666666666666)
|
||||
4HelixInsideOutLoose.scale(0.9166666666666666)
|
||||
4HelixPlanar.scale(0.9166666666666666)
|
||||
|
||||
# Note: "scale()" only effects the initial coordinates of
|
||||
# the molecule, not the force field parameters.
|
||||
# (If you plan to minimize the molecule, you don't need to
|
||||
# be so careful about the initial coordinates. In that case,
|
||||
# you don't have worry about "scale()". Feel free to remove.)
|
||||
|
||||
|
||||
} # 1beadProtSci2010 (namespace)
|
||||
|
||||
@ -1,198 +0,0 @@
|
||||
# Note:
|
||||
#
|
||||
# This example may require additional features to be added to LAMMPS. If
|
||||
# LAMMPS complains about an "Invalid pair_style", then download copy the
|
||||
# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
|
||||
# "src" directory and recompile LAMMPS.
|
||||
#
|
||||
# -------- Description --------
|
||||
#
|
||||
# This example contains an implementation of the DPPC lipid bilayer described in
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# and:
|
||||
# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
# J. Chem. Phys. 135, 244701 (2011)
|
||||
#
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
|
||||
# by harmonic bonds.
|
||||
#
|
||||
# A truncated version of this lipid (named "DLPC") has also been added.
|
||||
# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
|
||||
# parameterized to reproduce the correct behavior in a lipid bilayer mixture.
|
||||
#
|
||||
# Units:
|
||||
#
|
||||
# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
|
||||
# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
|
||||
# The "sigma" parameter corresponds to 7.5 angstroms.
|
||||
|
||||
|
||||
CGLipidBr2005 {
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "CGLipidBr2005" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
|
||||
#angle_style hybrid cosine/delta # <- used in the original article
|
||||
angle_style hybrid harmonic # <- prevents unphysical acute angle turns
|
||||
# Explanation:
|
||||
# angle_style cosine/delta: U(theta) = k*(1-cos(theta-theta0))
|
||||
# angle_style harmonic: U(theta) = k*(theta-theta0)^2
|
||||
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1130 &
|
||||
lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
|
||||
neighbor 2.0 multi # <- perhaps unnecessary
|
||||
communicate multi # <- perhaps unnecessary
|
||||
}
|
||||
|
||||
|
||||
DPPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
|
||||
$atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
$bond:b4 @bond:../backbone $atom:t2 $atom:t3
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
$angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
|
||||
}
|
||||
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
|
||||
} #DPPC
|
||||
|
||||
|
||||
DLPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
}
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
} #DLPC
|
||||
|
||||
|
||||
# Particles and properties shared by all lipid types:
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:int 200.0
|
||||
@atom:tail 200.0
|
||||
@atom:head 200.0 #<- Default head type. We may override it later.
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# -- Default settings/parameters for "CGLipidBr2005" --
|
||||
# (Hybrid bond & angle styles were used for portability.)
|
||||
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints
|
||||
# have been replaced by harmonic bonds.
|
||||
# The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
|
||||
bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# cosine/delta: U(theta) = k*(1-cos(theta-theta0))
|
||||
#angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
|
||||
# harmonic: U(theta) = k*(theta-theta0)^2 not (k/2)*(theta-theta0)^2
|
||||
angle_coeff @angle:backbone harmonic 9.85898661 180 #<-->30*eps
|
||||
}
|
||||
# I use a stiffer bond-angle than the original Brannigan & Brown 2005 paper
|
||||
# to attempt to compensate for the fact that here we are using a lipid
|
||||
# mixture of DPPC and DLPC. (The mixture of lipids introduces a great deal
|
||||
# of disorder into the bilayer which would not be present in a DPPC bilayer.
|
||||
# This causes pores to form. Increasing the angle stiffness prevents this.)
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# The interaction of "atom:int" with other "atom:int" atoms is given by
|
||||
# epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
|
||||
# r=3*sigma. This was implemented using pair_style table.
|
||||
# Unfortunately, mixing lj/charmm and "table" pair styles in the same
|
||||
# simulation is very inneficient.
|
||||
|
||||
pair_coeff @atom:int @atom:int table table_int.dat INT
|
||||
|
||||
# The interaction of tail beads with eachother is given by the formula below
|
||||
# and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
|
||||
pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# The interaction of head beads which all other beads is given by:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
|
||||
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
} # write_once("In Settings")
|
||||
|
||||
# Note: I divided epsilon by 4 to get "0.1643" because we are using the
|
||||
# "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
|
||||
# (The "es4k4l" coeffstyle is the default.) Using this convention makes it
|
||||
# easier to mix this coarse-grained lipid model with other molecular models.
|
||||
|
||||
|
||||
|
||||
} # CGLipidBr2005
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Note: This example has not been optimized for speed.
|
||||
#
|
||||
# Unfortunately, using both lj/charmm and "table" pair styles in the same
|
||||
# simulation seems to be very inneficient. (The simulation is twice as slow
|
||||
# as using only the "lj/charmm" pair styles for every pairwise interaction,
|
||||
# ...and about 25% slower than using "table" for every pairwise interaction.
|
||||
# However the lennard-jones pair styles support mixing, so we use them to
|
||||
# make it easier to run these molecules with other molecules which don't use
|
||||
# pair_table. I felt that portability was worth the extra 25% slow down.)
|
||||
|
||||
@ -1,29 +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)
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
rcut = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
if r > rcut:
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
@ -1,70 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# I realized later this is not what we want because although energy is conserved
|
||||
# all enrgies are shifted with respect to energies used in the Brannigan paper
|
||||
# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
|
||||
# (So don't use this.)
|
||||
|
||||
# Calculate and print a
|
||||
|
||||
def S(r, rc1, rc2, derivative=False):
|
||||
"""
|
||||
Calculate the switching function S(r) which decays continuously
|
||||
between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
|
||||
S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
|
||||
I'm using the same smoothing/switching cutoff function used by the CHARMM
|
||||
force-fields. (I'm even using the same code to implement it, taken
|
||||
from lammps charmm/coul/charmm pair style, rewritten in python.)
|
||||
|
||||
"""
|
||||
assert(rc2>rc1)
|
||||
rsq = r*r
|
||||
rc1sq = rc1*rc1
|
||||
rc2sq = rc2*rc2
|
||||
denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)))
|
||||
if rsq > rc2sq:
|
||||
return 0.0
|
||||
elif rsq < rc1sq:
|
||||
if derivative:
|
||||
return 0.0
|
||||
else:
|
||||
return 1.0
|
||||
else:
|
||||
rc2sq_minus_rsq = (rc2sq - rsq)
|
||||
rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
|
||||
if derivative:
|
||||
return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
|
||||
else:
|
||||
return (rc2sq_minus_rsq_sq *
|
||||
(rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
|
||||
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
Rc1 = 22.0
|
||||
Rc2 = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
# Multiply U(r) & F(r) by the smoothing/switch function
|
||||
U_r = U_r * S(r, Rc1, Rc2)
|
||||
F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
@ -1,207 +0,0 @@
|
||||
# Description:
|
||||
|
||||
# This example shows how to put a protein (inclusion) in a
|
||||
# lipid bilayer mixture composed of two different lipids (DPPC and DLPC).
|
||||
# The DPPC lipid model is described here:
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# The protein model is described here:
|
||||
# G. Bellesia, AI Jewett, and J-E Shea,
|
||||
# Protein Science, Vol19 141-154 (2010)
|
||||
# The new DLPC model is a truncated version of DPPC,
|
||||
# (Its behaviour has not been rigorously tested.)
|
||||
# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
|
||||
# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
|
||||
|
||||
# Note:
|
||||
# This example may require additional features to be added to LAMMPS.
|
||||
# If LAMMPS complains about an "Invalid pair_style", then copy the code
|
||||
# in the "additional_lammps_code" directory into your LAMMPS "src" directory
|
||||
# and recompile LAMMPS.
|
||||
|
||||
|
||||
|
||||
import "CGLipidBr2005.lt"
|
||||
|
||||
using namespace CGLipidBr2005
|
||||
|
||||
# The "= new random" syntax chooses one of several molecules at random
|
||||
|
||||
lipids = new random([DPPC, DLPC], [0.5,0.5], 1234) #"1234"=random_seed
|
||||
[13].move(7.5, 0, 0)
|
||||
[15].move(3.75, 6.49519, 0) # <-- hexagonal lattice
|
||||
[2].rot(180, 1, 0, 0) # <-- 2 monolayers
|
||||
|
||||
# Move all the lipds up to the center of the box
|
||||
|
||||
lipids[*][*][*].move(0,0,75.0)
|
||||
|
||||
|
||||
|
||||
|
||||
# Although this patch of lipids is not square or rectangular, (it looks
|
||||
# like a parallelogram), this is no longer the case after rectangular
|
||||
# periodic boundary conditions are applied. (Check by visualising in VMD.)
|
||||
|
||||
|
||||
write_once("Data Boundary") {
|
||||
0 97.5 xlo xhi
|
||||
0 97.42785792 ylo yhi
|
||||
0 150.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
# A note on geometry:
|
||||
# We want to create a bilayer arranged in a hexagonal lattice consisting of
|
||||
# 13 rows (each row is aligned with the x-axis)
|
||||
# 15 columns (aligned at a 60 degree angle from the x axis)
|
||||
# The lattice spacing is 7.5 Angstroms.
|
||||
# When wrapped onto a rectangular box, the dimensions of the system are:
|
||||
# 13 * 7.5 Angstroms in the X direction
|
||||
# 15 * 7.5*sqrt(3)/2 Angstroms in the Y direction
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# ------------------- protein inclusion ---------------------
|
||||
|
||||
import "1beadProtSci2010.lt"
|
||||
|
||||
using namespace 1beadProtSci2010
|
||||
|
||||
protein = new 4HelixInsideOut
|
||||
|
||||
protein.move(45.0, 25.98076211, 75.0)
|
||||
|
||||
|
||||
# Delete a hole in the membrane to create space for the protein.
|
||||
|
||||
delete lipids[4][2][*]
|
||||
delete lipids[6][2][*]
|
||||
delete lipids[3-6][3][*]
|
||||
delete lipids[3-5][4][*]
|
||||
delete lipids[2-5][5][*]
|
||||
delete lipids[2][6][*]
|
||||
delete lipids[4][6][*]
|
||||
|
||||
# Note: All atom types must include the full path (the name of
|
||||
# the namespace which defined them as well as the atom type name).
|
||||
# (This is because we are no longer inside that namespace.)
|
||||
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# -----------------------------------------------------------
|
||||
# -------- interactions between protein and lipids ----------
|
||||
# -----------------------------------------------------------
|
||||
|
||||
# Interactions between the protein and lipid atoms are usually
|
||||
# determined by mixing rules. (However this is not possible some
|
||||
# for atoms, such as the "int" atoms in the lipid model which
|
||||
# interact using -1/r^2 attraction.) Mixing rules do not make
|
||||
# sense for these atoms so we must explicitly define their
|
||||
# interaction with all other atoms.
|
||||
|
||||
# We want the hydrophobic interactions between hydrophobic residues in
|
||||
# the protein and beads the interior of the lipid to be energetically
|
||||
# similar to the attractive interactions between the lipid tails.
|
||||
#
|
||||
# Note: I made the width of the outward-facing protein beads slightly larger
|
||||
# ("12.5") whenever they interact with the "tail" beads in each lipid
|
||||
# (in order to make the protein wider there).
|
||||
# This hopefully relieves some of the internal negative pressure in the center
|
||||
# of the bilayer which can otherwise rip apart the protein or suck it into
|
||||
# the bilaer. (This is a hack, and I'm not sure if it is necessary.
|
||||
# For different protein or lipid models, you probably don't need this.)
|
||||
#
|
||||
# i j pairstylename eps sig K L
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# To help keep the protein from tilting 90 degrees and burying itself
|
||||
# within the lipid bilayer, we make the turn regions at either
|
||||
# end of the protein (strongly) attracted to the head groups
|
||||
# of the lipid. (In reality, they would probably be attracted
|
||||
# to the water as well.)
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
|
||||
# All other interactions between proteins and lipids are steric.
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
# -----------------------------------------------------------
|
||||
# -------- Modifications to the protein model: --------------
|
||||
# -----------------------------------------------------------
|
||||
#
|
||||
# Turn off attraction between the hydrophobic "@atom:sH" beads:
|
||||
# (These beads are located in the outside of a trans-membrane protein.)
|
||||
|
||||
pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
|
||||
|
||||
# (Why: These beads are only attracted to
|
||||
# each other in an aqueous environment)
|
||||
|
||||
# ... and
|
||||
# Turn ON attraction between the hydrophilic "@atom:sL" beads.
|
||||
# (These beads are located in the interior of a trans-membrane protein.)
|
||||
|
||||
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
|
||||
|
||||
# Why?
|
||||
# In reality, polar groups in the interior of trans-membrane
|
||||
# proteins do form hydrogen bonds with each other. This was
|
||||
# absent from the original protein model because, in an aqueous
|
||||
# environment, these groups preferentially interact with the water.
|
||||
#
|
||||
# Why is this necessary?
|
||||
# Shouldn't attraction between lipid tails and the protein create
|
||||
# an effective force which brings the hydrophilic beads together?
|
||||
# (similar to the hydrophobic effect, but in reverse?).
|
||||
# Answer:
|
||||
# Unlike an aqueous environment (~zero pressure, or +1atm), there is
|
||||
# a large negative pressure in the interior of some bilayer membrane
|
||||
# models (such as this one). Without some kind of direct attraction
|
||||
# between interior residues, the protein will get pulled apart.
|
||||
# (Perhaps the attractive force I am using is too strong?)
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
# Finally, we must combine the two force-field styles which were used for
|
||||
# the coarse-grained lipid and protein. To do that, we write one last time
|
||||
# to the "In Init" section. When reading the "Init" section LAMMPS will
|
||||
# read these commands last and this will override any earlier settings.
|
||||
|
||||
write_once("In Init") {
|
||||
# -- These styles override earlier settings --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid cosine/delta harmonic
|
||||
dihedral_style hybrid fourier
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
}
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,35 +0,0 @@
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# So, after typing "make yes-user-misc" in to the shell, ...
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
|
||||
# then you made a mistake in the instructions above.
|
||||
|
||||
|
||||
|
||||
# -- Init section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom definition section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run section --
|
||||
|
||||
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
write_restart system_after_min.rst
|
||||
@ -1,65 +0,0 @@
|
||||
# PREREQUISITES:
|
||||
#
|
||||
# You must use moltemplate.sh to create 3 files:
|
||||
# system.data system.in.init system.in.settings
|
||||
# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
|
||||
#
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# So, after typing "make yes-user-misc" in to the shell, ...
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
|
||||
# then you made a mistake in the instructions above.
|
||||
#
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
#minimize 1.0e-5 1.0e-7 500 2000
|
||||
|
||||
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
|
||||
|
||||
|
||||
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
|
||||
# (for the "epsilon" used by the coarse-grained lipid), and
|
||||
# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
# Note: We maintain the system system at constant (zero) tention
|
||||
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
|
||||
|
||||
|
||||
# optional (not sure if this helps):
|
||||
# balance x uniform y uniform
|
||||
|
||||
|
||||
run 100000
|
||||
|
||||
write_data system_after_npt.data
|
||||
@ -1,71 +0,0 @@
|
||||
# PREREQUISITES:
|
||||
#
|
||||
# 1) You must use moltemplate.sh to create 3 files:
|
||||
# system.data system.in.init system.in.settings
|
||||
# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
|
||||
# 2) You must equilibrate the system beforehand using "run.in.npt".
|
||||
# This will create the file "system_after_npt.data" which this file reads.
|
||||
# (Note: I have not verified that this equilibration protocol works well.)
|
||||
#
|
||||
# -------- LAMMPS REQUIREMENTS: ---------
|
||||
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
|
||||
# http://lammps.sandia.gov/doc/Section_start.html#start_3
|
||||
# 2) It also may require additional features and bug fixes for LAMMPS.
|
||||
# So, after typing "make yes-user-misc" in to the shell, ...
|
||||
# be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 3) Unpack it
|
||||
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 5) Compile LAMMPS.
|
||||
#
|
||||
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
|
||||
# then you made a mistake in the instructions above.
|
||||
#
|
||||
# ------------------------------- Initialization Section --------------------
|
||||
|
||||
include system.in.init
|
||||
|
||||
# ------------------------------- Atom Definition Section -------------------
|
||||
|
||||
|
||||
# Read the coordinates generated by an earlier NPT simulation
|
||||
|
||||
read_data system_after_npt.data
|
||||
|
||||
# (The "write_restart" and "read_restart" commands were buggy in 2012,
|
||||
# but they should work also. I prefer "write_data" and "read_data".)
|
||||
|
||||
|
||||
# ------------------------------- Settings Section --------------------------
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# ------------------------------- Run Section -------------------------------
|
||||
|
||||
|
||||
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnve all nve
|
||||
|
||||
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
|
||||
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
|
||||
#restart 500000
|
||||
|
||||
run 10000000
|
||||
|
||||
|
||||
write_data system_after_nvt.data
|
||||
|
||||
# (The "write_restart" and "read_restart" commands were buggy in 2012,
|
||||
# but they should work also.)
|
||||
|
||||
@ -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.
|
||||
|
||||
|
||||
-------------
|
||||
|
||||
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
|
||||
@ -1,33 +0,0 @@
|
||||
# --- Running LAMMPS ---
|
||||
# -- Prerequisites: --
|
||||
# The "run.in.nvt" file is a LAMMPS input script containing
|
||||
# references to the input scripts and data files
|
||||
# you hopefully have created earlier with moltemplate.sh:
|
||||
# system.in.init, system.in.settings, system.data, and table_int.dat
|
||||
# If not, carry out the instructions in "README_setup.sh".
|
||||
#
|
||||
# -- Instructions: --
|
||||
# If "lmp_linux" is the name of the command you use to invoke lammps,
|
||||
# then you would run lammps on these files this way:
|
||||
|
||||
|
||||
lmp_linux -i run.in.npt # Run a simulation at constant pressure (tension)
|
||||
|
||||
#or
|
||||
|
||||
lmp_linux -i run.in.nvt # Run a simulation at constant volume
|
||||
|
||||
#(Note: The constant volume simulation lacks pressure equilibration. These are
|
||||
# completely separate simulations. The results of the constant pressure
|
||||
# simulation are ignored when beginning the simulation at constant volume.
|
||||
# This can be fixed. Read "run.in.nvt" for equilibration instructions.)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# If you have compiled the MPI version of lammps, you can run lammps in parallel
|
||||
#mpirun -np 4 lmp_linux -i run.in.npt
|
||||
#or
|
||||
#mpirun -np 4 lmp_linux -i run.in.nvt
|
||||
# (assuming you have 4 processors available)
|
||||
@ -1,28 +0,0 @@
|
||||
# Use these commands to generate the LAMMPS input script and data file
|
||||
# (and other auxilliary files):
|
||||
|
||||
|
||||
# Create LAMMPS input files this way:
|
||||
cd moltemplate_files
|
||||
|
||||
# run moltemplate
|
||||
|
||||
moltemplate.sh system.lt
|
||||
|
||||
# This will generate various files with names ending in *.in* and *.data.
|
||||
# These files are the input files directly read by LAMMPS. Move them to
|
||||
# the parent directory (or wherever you plan to run the simulation).
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# The "table_int.dat" file contains tabular data for the lipid INT-INT atom
|
||||
# 1/r^2 interaction. We need it too. (This slows down the simulation by x2,
|
||||
# so I might look for a way to get rid of it later.)
|
||||
cp -f table_int.dat ../
|
||||
|
||||
# Optional:
|
||||
# The "./output_ttree/" directory is full of temporary files generated by
|
||||
# moltemplate. They can be useful for debugging, but are usually thrown away.
|
||||
rm -rf output_ttree/
|
||||
|
||||
cd ../
|
||||
@ -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.)
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 4.8 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 57 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 36 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 61 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 5.7 KiB |
@ -1,191 +0,0 @@
|
||||
# Note:
|
||||
#
|
||||
# This example may require additional features to be added to LAMMPS. If
|
||||
# LAMMPS complains about an "Invalid pair_style", then download copy the
|
||||
# "additional_lammps_code" from moltemplate.org, unpack it into your LAMMPS
|
||||
# "src" directory and recompile LAMMPS.
|
||||
#
|
||||
# -------- Description --------
|
||||
#
|
||||
# This example contains an implementation of the DPPC lipid bilayer described in
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
# and:
|
||||
# M.C. Watson, E.S. Penev, P.M. Welch, and F.L.H. Brown
|
||||
# J. Chem. Phys. 135, 244701 (2011)
|
||||
#
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints have been replaced
|
||||
# by harmonic bonds.
|
||||
#
|
||||
# --- DLPC lipids ---
|
||||
# A truncated version of the DPPC lipid (named "DLPC") has also been added.
|
||||
# Unlike the original "DPPC" molecule model, "DLPC" has not been carefully
|
||||
# parameterized to reproduce the correct behavior in a lipid bilayer/mixture.
|
||||
# (You may need to stiffen the bond-angle forces to make it behave correctly,
|
||||
# but I did not do this here.)
|
||||
#
|
||||
# Units:
|
||||
#
|
||||
# The "epsilon" parameter in their model is approximately 2.75 kJ/mole
|
||||
# ( = 0.657265774378585 kCal/mole, using 1kCal=4.184kJ)
|
||||
# The "sigma" parameter corresponds to 7.5 angstroms.
|
||||
#
|
||||
#
|
||||
# The new DLPC model is a truncated version of DPPC,
|
||||
# (Its behaviour has not been rigorously tested.)
|
||||
|
||||
|
||||
CGLipidBr2005 {
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
# -- Default styles for "CGLipidBr2005" --
|
||||
units real
|
||||
atom_style full
|
||||
# (Hybrid force field styles were used for portability.)
|
||||
bond_style hybrid harmonic
|
||||
angle_style hybrid cosine/delta
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
pair_style hybrid table linear 1130 &
|
||||
lj/charmm/coul/charmm/inter es4k4l 14.5 15
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
|
||||
|
||||
neighbor 2.0 multi # <- perhaps unnecessary
|
||||
communicate multi # <- perhaps unnecessary
|
||||
}
|
||||
|
||||
|
||||
DPPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 33.75 # DPPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 26.25
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 18.75
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 11.25
|
||||
$atom:t3 $mol:. @atom:../tail 0.0 1.00 0.00 3.75
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
$bond:b4 @bond:../backbone $atom:t2 $atom:t3
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
$angle:a3 @angle:../backbone $atom:t1 $atom:t2 $atom:t3
|
||||
}
|
||||
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
|
||||
} #DPPC
|
||||
|
||||
|
||||
DLPC {
|
||||
write("Data Atoms") {
|
||||
$atom:h $mol:. @atom:head 0.0 0.00 0.00 30.00 # DLPC head atom
|
||||
$atom:i $mol:. @atom:../int 0.0 -1.00 0.00 22.50
|
||||
$atom:t1 $mol:. @atom:../tail 0.0 1.00 0.00 15.00
|
||||
$atom:t2 $mol:. @atom:../tail 0.0 -1.00 0.00 7.50
|
||||
}
|
||||
write("Data Bonds") {
|
||||
$bond:b1 @bond:../backbone $atom:h $atom:i
|
||||
$bond:b2 @bond:../backbone $atom:i $atom:t1
|
||||
$bond:b3 @bond:../backbone $atom:t1 $atom:t2
|
||||
}
|
||||
write("Data Angles") {
|
||||
$angle:a1 @angle:../backbone $atom:h $atom:i $atom:t1
|
||||
$angle:a2 @angle:../backbone $atom:i $atom:t1 $atom:t2
|
||||
}
|
||||
# Define properties of the local (lipid-specific) atom:head type atom:
|
||||
write_once("Data Masses") {
|
||||
@atom:head 200.0
|
||||
}
|
||||
write_once("In Settings") {
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:../int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
}
|
||||
} #DLPC
|
||||
|
||||
|
||||
# Particles shared by all lipid types
|
||||
write_once("Data Masses") {
|
||||
@atom:int 200.0
|
||||
@atom:tail 200.0
|
||||
@atom:head 200.0 #<- Default head type. We may override it later.
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# -- Default settings/parameters for "CGLipidBr2005" --
|
||||
# (Hybrid bond & angle styles were used for portability.)
|
||||
|
||||
# As in Watson(JCP 2011), rigid bond-length constraints
|
||||
# have been replaced by harmonic bonds.
|
||||
# The k_theta parameter should lie in between 5*epsilon and 10*epsilon.
|
||||
bond_coeff @bond:backbone harmonic 116.847 7.5 #<--2*5000*eps/sig^2
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
angle_coeff @angle:backbone cosine/delta 4.60086042 180 #<-- 7*eps
|
||||
#angle_coeff @angle:backbone cosine/delta 6.57265774 180 #<-- 10*eps
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
|
||||
# The interaction of "atom:int" with other "atom:int" atoms is given by
|
||||
# epsilon*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2), shifted and cutoff at
|
||||
# r=3*sigma. This was implemented using pair_style table.
|
||||
# Unfortunately, mixing lj/charmm and "table" pair styles in the same
|
||||
# simulation is very inneficient.
|
||||
|
||||
pair_coeff @atom:int @atom:int table table_int.dat INT
|
||||
|
||||
# The interaction of tail beads with eachother is given by the formula below
|
||||
# and with other atoms ...using Lorenz-Berthelot and "repulsive wins" rules:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 1.0*(sigma/r)^6),
|
||||
pair_coeff @atom:tail @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
pair_coeff @atom:int @atom:tail lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
|
||||
|
||||
# The interaction of head beads which all other beads is given by:
|
||||
# epsilon*(0.4*(sigma/r)^12 - 0.0*(sigma/r)^6),
|
||||
|
||||
pair_coeff @atom:head @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
pair_coeff @atom:int @atom:head lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
|
||||
|
||||
|
||||
} # write_once("In Settings")
|
||||
|
||||
# Note: I divided epsilon by 4 to get "0.1643" because we are using the
|
||||
# "es4k4l" coeffstyle, corresponding to U(r)=eps(4*K*(s/r)^12 + 4*L*(s/r)^6)
|
||||
# (The "es4k4l" coeffstyle is the default.) Using this convention makes it
|
||||
# easier to mix this coarse-grained lipid model with other molecular models.
|
||||
|
||||
|
||||
|
||||
} # CGLipidBr2005
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# Note: This example has not been optimized for speed.
|
||||
#
|
||||
# Unfortunately, using both lj/charmm and "table" pair styles in the same
|
||||
# simulation seems to be very inneficient. (The simulation is twice as slow
|
||||
# as using only the "lj/charmm" pair styles for every pairwise interaction,
|
||||
# ...and about 25% slower than using "table" for every pairwise interaction.
|
||||
# However the lennard-jones pair styles support mixing, so we use them to
|
||||
# make it easier to run these molecules with other molecules which don't use
|
||||
# pair_table. I felt that portability was worth the extra 25% slow down.)
|
||||
|
||||
@ -1,29 +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)
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
rcut = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
if r > rcut:
|
||||
U_r = 0.0
|
||||
F_r = 0.0
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
@ -1,70 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
# Calculate a table of pairwise energies and forces between "INT" atoms
|
||||
# in the lipid membrane model described in
|
||||
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
|
||||
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
|
||||
# I realized later this is not what we want because although energy is conserved
|
||||
# all enrgies are shifted with respect to energies used in the Brannigan paper
|
||||
# (by 0.27 kCal/mole) and the later Watson JCP 2011 paper (by 0.224 kCal/mole).
|
||||
# (So don't use this.)
|
||||
|
||||
# Calculate and print a
|
||||
|
||||
def S(r, rc1, rc2, derivative=False):
|
||||
"""
|
||||
Calculate the switching function S(r) which decays continuously
|
||||
between 1 and 0 in the range from rc1 to rc2 (rc2>rc1):
|
||||
S(r) = (rc2^2 - r^2)^2 * (rc2^2 + 2*r^2 - 3*rc1^2) / (rc2^2-rc1^2)^3
|
||||
I'm using the same smoothing/switching cutoff function used by the CHARMM
|
||||
force-fields. (I'm even using the same code to implement it, taken
|
||||
from lammps charmm/coul/charmm pair style, rewritten in python.)
|
||||
|
||||
"""
|
||||
assert(rc2>rc1)
|
||||
rsq = r*r
|
||||
rc1sq = rc1*rc1
|
||||
rc2sq = rc2*rc2
|
||||
denom_lj_inv = (1.0 / ((rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)*
|
||||
(rc2sq-rc1sq)))
|
||||
if rsq > rc2sq:
|
||||
return 0.0
|
||||
elif rsq < rc1sq:
|
||||
if derivative:
|
||||
return 0.0
|
||||
else:
|
||||
return 1.0
|
||||
else:
|
||||
rc2sq_minus_rsq = (rc2sq - rsq)
|
||||
rc2sq_minus_rsq_sq = rc2sq_minus_rsq * rc2sq_minus_rsq
|
||||
if derivative:
|
||||
return (12.0 * rsq * rc2sq_minus_rsq * (rsq-rc1sq) * denom_lj_inv)
|
||||
else:
|
||||
return (rc2sq_minus_rsq_sq *
|
||||
(rc2sq + 2.0*rsq - 3.0*rc1sq) * denom_lj_inv)
|
||||
|
||||
|
||||
def U(r, eps, sigma):
|
||||
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
|
||||
|
||||
def F(r, eps, sigma):
|
||||
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
|
||||
|
||||
epsilon = 2.75/4.184 # kCal/mole
|
||||
sigma = 7.5
|
||||
Rmin = 0.02
|
||||
Rmax = 22.6
|
||||
Rc1 = 22.0
|
||||
Rc2 = 22.5
|
||||
N = 1130
|
||||
|
||||
for i in range(0,N):
|
||||
r = Rmin + i*(Rmax-Rmin)/(N-1)
|
||||
U_r = U(r, epsilon, sigma)
|
||||
F_r = F(r, epsilon, sigma)
|
||||
# Multiply U(r) & F(r) by the smoothing/switch function
|
||||
U_r = U_r * S(r, Rc1, Rc2)
|
||||
F_r = U_r * S(r, Rc1, Rc2, True) + F_r * S(r, Rc1, Rc2, False)
|
||||
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
|
||||
|
||||
@ -1,94 +0,0 @@
|
||||
# Description:
|
||||
|
||||
# This constructs a bilayer constructed from coarse-grained DPPC lipids
|
||||
# (implicit solvent). The DPPC lipid model is described here:
|
||||
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
|
||||
# Physical Review E, Vol 72, 011915 (2005)
|
||||
#
|
||||
# NOTE: There is an example of a 50%/50% DPPC & DLPC mixture
|
||||
# in the "membrane+protein" and "vesicle" examples.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
import "CGLipidBr2005Orig.lt"
|
||||
|
||||
using namespace CGLipidBr2005
|
||||
|
||||
lipids = new DPPC [32].move(7.5, 0, 0)
|
||||
[37].move(3.75, 6.49519, 0)
|
||||
[2].rot(180, 1, 0, 0)
|
||||
|
||||
|
||||
# Move the lipds up to the center of the box
|
||||
lipids[*][*][*].move(0,0,75.0)
|
||||
|
||||
|
||||
# Although this patch of lipids is not square or rectangular, (it looks
|
||||
# like a parallelogram), this is no longer the case after rectangular
|
||||
# periodic boundary conditions are applied. We apply them below:
|
||||
# width: 240 = 32*7.5
|
||||
# height: 240.322 = 37*6.49519
|
||||
|
||||
write_once("Data Boundary") {
|
||||
0 240 xlo xhi
|
||||
0 240.322 ylo yhi
|
||||
0 150.0 zlo zhi
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# -------------- File ends here. Only comments below.-------------------
|
||||
|
||||
# ------------------------------------
|
||||
# ------------- COMMENTS: ------------
|
||||
# ------------------------------------
|
||||
#
|
||||
# A note on geometry:
|
||||
# We want to create a bilayer arranged in a hexagonal lattice consisting of
|
||||
# 32 rows (each row is aligned with the x-axis)
|
||||
# 37 columns (aligned at a 60 degree angle from the x axis)
|
||||
# The lattice spacing is 8.0 Angstroms ( ~= 0.95*sigma*2^(1/6), where sigma=7.5)
|
||||
# When wrapped onto a rectangular box, the dimensions of the system are:
|
||||
# 32 * 7.5 Angstroms in the X direction
|
||||
# 37 * 7.5*sqrt(3)/2 Angstroms in the Y direction
|
||||
# ------------------------------------
|
||||
#
|
||||
# Below I show simple ways to create a lipid bilayer:
|
||||
#
|
||||
# 1) If you just want to make lipid bilayer out of DPPC,
|
||||
# without specifying the location of each lipid, you could use this syntax:
|
||||
# lipids = new DPPC [32][37][2] # 3-D array
|
||||
# Later you can load in the coordinates of the lipds from a PDB file.
|
||||
# Alternately you could also use a 1-dimensional array:
|
||||
# lipids = new DPPC [2368] # 1-D array. Note: 2368 = 32 x 37 x 2
|
||||
# It does not matter as long as the number of lipids is correct.
|
||||
# Multidimensional arrays are only useful if you plan to apply independent
|
||||
# coordinate transformations to each row and column and monolayer. See below:
|
||||
#
|
||||
# 2) Instead of loading a PDB file later, we can directly specify the location
|
||||
# of each DPPC lipid in the LT file itself. For lipid bilayers, this is
|
||||
# easy, because the bilayer structure resembles 2 planar lattices.
|
||||
# We can use "move" commands to place each lipid, and the "rot" command
|
||||
# to turn the lipids in one of the monolayers upside down.
|
||||
#
|
||||
# lipids = new DPPC [32].move(7.5, 0, 0)
|
||||
# [37].move(3.75, 6.49519, 0)
|
||||
# [2].rot(180, 1, 0, 0)
|
||||
#
|
||||
# 3) If you want to create a bilayer from a mixture of DPPC and DLPC, you must
|
||||
# replace "DPPC" in the command above with random([DPPC,DLPC],[0.5,0.5],12345)
|
||||
# Here "0.5,0.5" are the probabilities for each molecule type, and "12345"
|
||||
# is an optional random seed.
|
||||
# lipids = new random([DPPC,DLPC], [0.5,0.5], 12345)
|
||||
# [32].move(7.5, 0, 0)
|
||||
# [37].move(3.75, 6.49519, 0)
|
||||
# [2].rot(180, 1, 0, 0)
|
||||
#
|
||||
File diff suppressed because it is too large
Load Diff
@ -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
|
||||
@ -1,57 +0,0 @@
|
||||
# -------- REQUIREMENTS: ---------
|
||||
# 1) This example may require additional features and bug fixes for LAMMPS.
|
||||
# Be sure to download and copy the "additional_lammps_code" from
|
||||
# http://moltemplate.org (upper-left corner menu)
|
||||
# 2) Unpack it
|
||||
# 3) copy the .cpp and .h files to the src folding of your lammps installation.
|
||||
# 4) Compile LAMMPS.
|
||||
#
|
||||
# (If LAMMPS complains about an "Invalid pair_style"
|
||||
# then you made a mistake in the instructions above.)
|
||||
#
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
read_data system.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 5000 traj_npt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
|
||||
|
||||
|
||||
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
|
||||
# for the "epsilon" used by the coarse-grained lipid.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
# Note: We maintain the system system at constant (zero) tention
|
||||
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
|
||||
|
||||
|
||||
# optional (not sure if this helps):
|
||||
# balance x uniform y uniform
|
||||
|
||||
|
||||
#restart 1000000
|
||||
|
||||
run 2000000
|
||||
|
||||
write_restart system_after_npt.rst
|
||||
|
||||
@ -1,53 +0,0 @@
|
||||
# ------------------------------- Initialization Section --------------------
|
||||
|
||||
include system.in.init
|
||||
|
||||
# ------------------------------- Atom Definition Section -------------------
|
||||
|
||||
|
||||
# Normally, I would minimize the system and equilibrate the system at constant
|
||||
# pressure and temperature beforehand. If you run lammps with "run.in.npt",
|
||||
# it will generate a restart file "system_after_npt.rst" with reasonable
|
||||
# coordinates at that temperature and pressure. Then we could load it now:
|
||||
#
|
||||
#read_restart system_after_npt.rst
|
||||
#
|
||||
# Unfortunately the LAMMPS "read_restart" command has been undependable over
|
||||
# the past year (2012), and I feel it is safer to remove it from the examples.
|
||||
# Instead, for this example, I just read the raw coordinates generated by
|
||||
# moltemplate (and the default volume). (I get fewer questions this way.)
|
||||
# However you should never run any liquid simulations at constant volume without
|
||||
# pressure equilibration first. Hopefully in the future "read_restart" will
|
||||
# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
|
||||
|
||||
read_data system.data
|
||||
|
||||
# ------------------------------- Settings Section --------------------------
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# ------------------------------- Run Section -------------------------------
|
||||
|
||||
|
||||
timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
|
||||
dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
|
||||
thermo_style custom step temp pe etotal vol epair ebond eangle
|
||||
thermo 1000 # time interval for printing out "thermo" data
|
||||
|
||||
|
||||
fix fxlan all langevin 300.0 300.0 120 48279
|
||||
fix fxnve all nve
|
||||
|
||||
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
|
||||
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
|
||||
# Note: The langevin damping parameter "120" corresponds to
|
||||
# the 0.12ps damping time used in Watson et. al JCP 2011.
|
||||
|
||||
#restart 1000000
|
||||
|
||||
run 1000000
|
||||
|
||||
write_restart system_after_nvt.rst
|
||||
|
||||
@ -1,47 +0,0 @@
|
||||
This is an implementation of the "two-stage" model used by Maxim Imakaev
|
||||
in the Naumova et Al 2013 Science paper on metaphase chromatin.
|
||||
(Download the supplemental materials section and scroll down to the section:
|
||||
"Two-stage process: linear compaction - axial compression")
|
||||
|
||||
---- SMALL MODIFICATION ----
|
||||
|
||||
Unlike that study, I did not use "softened" Lennard-Jones potentials
|
||||
(which allow the chains to pass through each other).
|
||||
|
||||
--- Why use moltemplate? ---
|
||||
|
||||
Honestly, you don't need to use moltemplate to build this polymer.
|
||||
It is almost counter-productive to use moltemplate to build this kind of
|
||||
polymer because it is so simple. (The polymer has only 1 bead per atom.
|
||||
It just makes it more complicated to introduce all these extra
|
||||
files including monomer.lt, condensin.lt and system.lt, especially considering
|
||||
that system.lt is a complex file which is generated by a separate script.)
|
||||
|
||||
However building the sytem using moltemplate may pay off if you
|
||||
replace each point-like monomer with a multi-atom molecule later on.
|
||||
(Right now, using moltemplate to build this system is sort of overkill.
|
||||
I'll post an example of building more complex models of chromatin eventually.)
|
||||
|
||||
---- 30-nm fiber model: ----
|
||||
|
||||
Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.
|
||||
|
||||
For the 10nm model,
|
||||
n=128000,
|
||||
L=200,
|
||||
U(alpha)=5*(1 - cos(alpha))
|
||||
bond_length=1.0 (=10nm)
|
||||
sigma=1.0 (particle radius = 10nm)
|
||||
|
||||
30nm-fiber model details:
|
||||
"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."
|
||||
|
||||
I interpret this to mean that, for the 30nm model,
|
||||
n=128000/4.25~=30117 (however I rounded up to 32768=2^15)
|
||||
L=200/4.25~=47 (however I rounded up to 51)
|
||||
U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647)
|
||||
|
||||
To increase the volume by a factor o 4.25, I increase both the diameter of each
|
||||
bead (the "sigma" parameter), and the bond-lengths connecting them from
|
||||
1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm).
|
||||
|
||||
@ -1,29 +0,0 @@
|
||||
---------------
|
||||
The average diameter of a mammalian cell nucleus is is 6 micrometers (μm),
|
||||
which occupies about 10% of the total cell volume.
|
||||
|
||||
(See "Molecular Biology of the Cell, Chapter 4, pages 191–234 (4th ed.)", by
|
||||
Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, Peter Walter, 2002)
|
||||
|
||||
... of that, 25% of it is occupied by the nucleolus
|
||||
http://en.wikipedia.org/wiki/Nucleolus
|
||||
("citation needed")
|
||||
---------------
|
||||
|
||||
From the supplemental material for the original HiC paper
|
||||
(Lieberman-Aiden et al., Science 2009)
|
||||
|
||||
Appendix 1.
|
||||
Estimate of the Volume Fraction of Chromatin in Human Cells
|
||||
In the simulations we sought to obtain an ensemble of structures that, in their statistical properties, resemble some of the features of chromatin arrangement in the cell. Below we demonstrate that chromatin occupies a significant fraction of cell volume, a property that we reproduced in simulations. Taking the nuclear diameter of a tissue culture cell to be 5-10um, and assuming close to a spherical shape we obtain the volume in the range 50-500 um^3, with a (geometric) mean of ~160 um^3. If we assume that the chromatin is built of DNA wrapped around nucleosomes, then we have 6x10^9bp/200bp=3x10^7 nucleosomes. Each may be approximated as a cylinder ~10nm in diameter and ~5nm in height, suggesting a volume of about 500nm3 each. The linker DNA after each nucleosome is about 50bps long, suggesting a volume of about 50*0.34nm*3.14*1nm^2=50nm^3. Thus the total volume of chromatin = 550x3x10^7 =16 um^3, or ~10% (3-23%) of the nuclear volume. This strikingly large volume fraction is itself a significant underestimate, since we ignored, among other things, all other DNA-bound proteins. Note that any further packing or localization of chromatin inside the nucleus will increase local density.
|
||||
---- This next section mostly only justifies why they ----
|
||||
---- they did not stop the simulation when the globules ----
|
||||
---- were fully crumpled (ie with uniform density) ----
|
||||
In our simulations, the radius of the final crumpled globule was R≈12.5 and the volume V≈8000 cubic units. The total volume of the 4000 monomers, 1 unit in diameters each, is V≈2000. This implies a volume fraction of about 25%, which is consistent with the volume fraction estimated above.
|
||||
---- ----
|
||||
|
||||
Appendix 2.
|
||||
Monomer length in base pairs
|
||||
Each monomer of the chain corresponds to a fragment of chromatin that equals the Kuhn length of the chromatin fiber, i.e. approximately twice the persistence length of the fiber. Although the persistence length of the chromatin fiber is unknown it can be estimated using the following arguments. DNA is packed into nucleosomes, where 150 bps are wrapped around the histone core and do not contribute to flexibility of the fiber. The linker DNA of about 50 bps that connects consecutive nucleosomes is bendable, and is the source of flexibility in the fiber. Since the persistence length of double-stranded DNA is 150 bps, an equally flexible region of the nucleosomal DNA should contain 3 linkers, i.e. 3 consecutive nucleosomes packing about 600 bps of DNA. The excluded volume of the nucleosomes, nucleosome interactions, and other DNA-bound proteins can make the fiber less flexible or prohibit certain conformation and may tend to increase the persistence length of the fiber. Using this estimated lower bound estimate for the persistence length, we obtain the Kuhn length of the equivalent freely-jointed chain to be 6 nucleosomes, or ~ 1200bp. A simulated chain of 4000 monomers corresponds to 4.8Mb of packed DNA. The size of each monomer was chosen such that its volume is equal to (or slightly above) that of 6 nucleosomes (V=6 x 600 nm^3); thus the radius of the spherical monomer is R=10nm. The diameter of each globule shown in Figure 4 is about 200 nm.
|
||||
|
||||
|
||||
@ -1,7 +0,0 @@
|
||||
# Run lammps using the following 3 commands:
|
||||
# (assuming "lmp_linux" is the name of your LAMMPS binary)
|
||||
|
||||
lmp_linux -i run.in.min
|
||||
lmp_linux -i run.in.stage1
|
||||
lmp_linux -i run.in.stage2
|
||||
|
||||
@ -1,58 +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
|
||||
|
||||
# First, rescale and interpolate the positions
|
||||
# where the monomers will be located. (This step is
|
||||
# not needed if the coords_orig.raw file already has correct coordinates.)
|
||||
|
||||
./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw
|
||||
|
||||
# Then, build the "system.lt" file
|
||||
|
||||
./generate_system_lt.py 32768 51 < coords.raw > system.lt
|
||||
|
||||
# 32768 is the number of monomers in the polymer
|
||||
# (which may be different from the number of coordinates
|
||||
# in the "coords_orig.raw" file) This number will vary
|
||||
# depending on how long you want the polymer to be.
|
||||
# The second argument "51" is the average interval between
|
||||
# condensin anchors (IE the "loop size" in monomers.)
|
||||
|
||||
|
||||
# Run moltemplate
|
||||
|
||||
moltemplate.sh system.lt -a "@bond:stage1 1" \
|
||||
-a "@bond:stage2 2" \
|
||||
-a "@atom:Monomer/A 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).
|
||||
#
|
||||
# We used the "-a" command to set the variable @bond:condensin to "2"
|
||||
# because we will refer to it later in the "run.in" LAMMPS input script.
|
||||
# (Of coarse, LAMMPS knows nothing about moltemplate variables,
|
||||
# so in that file we refer to it as dihedral type "1")
|
||||
|
||||
mv -f system.in* system.data ../
|
||||
|
||||
# We also need the table of bond forces used during "stage 2".
|
||||
# (Like the system.data and the various input scripts, this file is needed by
|
||||
# LAMMPS, so we need to copy it to the directory where we will run the sim.)
|
||||
cp -f table_bonds_stage2.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/
|
||||
|
||||
# Optional:
|
||||
# Remove the "system.lt" file created by "generate_system_lt.py"
|
||||
#rm -f system.lt
|
||||
|
||||
cd ../
|
||||
|
||||
@ -1,131 +0,0 @@
|
||||
NOTE: VMD DOES NOT ALLOW YOU TO VISUALIZE SYSTEMS WITH MANY BONDS ATTACHED
|
||||
TO EACH ATOM. (IF IT DID, THE RESULTS WOULD BE UGLY ANWAY.)
|
||||
|
||||
HOWEVER THIS MODEL ATTACHES APPROXIMATELY 60 BONDS TO EACH CONDENSIN ATOM.
|
||||
IN ORDER TO PULL THE CONDENSIN MONOMERS TOGETHER. YOU MUST DELETE THOSE
|
||||
BONDS (of type "1" or "2") FROM THE "system.data" FILE BEFORE YOU CARRY
|
||||
OUT THE COMMANDS BELOW. (...And backup your "system.data" file. You'll need
|
||||
all the bonds when you run the simulations.)
|
||||
|
||||
-------------- COLORS ---------------
|
||||
In order to show how the polymer is distributed along the length of the
|
||||
cylinder, I recommend to select the
|
||||
Graphics->Graphical Representations
|
||||
menu option, and select "Index" from the "Coloring Method" pull-down menu.
|
||||
|
||||
After doing this, you can switch from a red-white-blue scheme, to a
|
||||
rainbow ("jet") scheme, by selecting the Extensions->Tk Console menu option
|
||||
and loading the "vmd_colorscale_jet.tcl" file located in the "images" directory.
|
||||
-------------------------------------------
|
||||
|
||||
First, if you have not done so, download and install VMD:
|
||||
|
||||
http://www.ks.uiuc.edu/Research/vmd/
|
||||
http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD
|
||||
|
||||
|
||||
------- To view a lammps trajectory in VMD --------
|
||||
|
||||
The system coordinates are initialy stored in a LAMMPS' ".data" file.
|
||||
(If that file was built with moltemplate, it will be named "system.data".)
|
||||
|
||||
The first step is to view that file.
|
||||
Then you should create a ".psf" file
|
||||
(The .psf file is necessary after you run the simulation
|
||||
for viewing trajectories.)
|
||||
|
||||
1) Build a PSF file for use in viewing with VMD
|
||||
|
||||
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
|
||||
|
||||
You will see a snapshot of the system on the screen.
|
||||
(presumably the initial conformation at t=0)
|
||||
|
||||
2)
|
||||
|
||||
Later once you have run a simulation,
|
||||
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
|
||||
(It usually has names like "traj.lammpstrj". It depends on how you saved it.)
|
||||
If necessary, for "file type" select: "LAMMPS Trajectory".
|
||||
(However VMD should recognize the file type by the file extension.)
|
||||
Load it.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
##################### PERIODIC BOUNDARY CONDITIONS #####################
|
||||
If you are only simulating a single molecule and you are not
|
||||
using periodic boundary conditions, then ignore everything below.
|
||||
########################################################################
|
||||
|
||||
---- A note on trajectory format: -----
|
||||
If the trajectory is the standard LAMMPS format, (aka a "DUMP" file with
|
||||
a ".lammpstrj" extension), then it's a good idea when you run the simulation
|
||||
to tell LAMMPS you want to store the information needed for showing periodic
|
||||
boundary conditions. (Even if you are not using periodic boundaries.
|
||||
It never hurts to include a tiny bit of extra information.) To do that,
|
||||
I've been using this command in my LAMMPS scripts to create the trajectories:
|
||||
|
||||
dump 1 all custom 5000 traj.lammpstrj id mol type x y z ix iy iz
|
||||
|
||||
(Also: 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 visually without breaking molecules in half. Again
|
||||
you don't need to worry about this if you are not using periodic boundaries.)
|
||||
|
||||
|
||||
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 {-0.5 -0.5 -0.5}
|
||||
pbc box -shiftcenterrel {-0.5 -0.5 -0.5}
|
||||
|
||||
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.)
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 40 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 25 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 78 KiB |
@ -1,87 +0,0 @@
|
||||
|
||||
proc lerpcolor { col1 col2 alpha } {
|
||||
set dc [vecsub $col2 $col1]
|
||||
set nc [vecadd $col1 [vecscale $dc $alpha]]
|
||||
return $nc
|
||||
}
|
||||
|
||||
proc coltogs { col } {
|
||||
foreach {r g b} $col {}
|
||||
set gray [expr ($r + $g + $b) / 3.0]
|
||||
return [list $gray $gray $gray]
|
||||
}
|
||||
|
||||
proc jet_tricolor_scale {} {
|
||||
display update off
|
||||
set mincolorid [expr [colorinfo num] - 1]
|
||||
set maxcolorid [expr [colorinfo max] - 1]
|
||||
set colrange [expr $maxcolorid - $mincolorid]
|
||||
set colhalf [expr $colrange / 2]
|
||||
for {set i $mincolorid} {$i < $maxcolorid} {incr i} {
|
||||
set colpcnt [expr ($i - $mincolorid) / double($colrange)]
|
||||
|
||||
# The following color definitions for "jet" sort-of came from:
|
||||
#http://stackoverflow.com/questions/7706339/grayscale-to-red-green-blue-matlab-jet-color-scale
|
||||
# but it was missing "green", so I inserted a green somewhere in the middle.
|
||||
|
||||
# darkblue/violet 0.0
|
||||
set color0 { 0.08 0.0 0.77 }
|
||||
|
||||
# blue 0.19
|
||||
set color1 { 0.0 0.0 1.0 }
|
||||
|
||||
# cyan 0.34
|
||||
set color2 { 0.0 1.0 1.0 }
|
||||
|
||||
# turquoise 0.4001
|
||||
set color3 { 0.0 1.0 0.78 }
|
||||
|
||||
# green 0.445
|
||||
set color4 { 0.0 1.0 0.0 }
|
||||
|
||||
# chartreuse 0.535
|
||||
set color5 { 0.875 1.0 0.0 }
|
||||
|
||||
# yellow 0.69
|
||||
set color6 { 1.0 1.0 0.0 }
|
||||
|
||||
# orange 0.73
|
||||
set color7 { 1.0 0.25 0.0 }
|
||||
|
||||
# red 0.755
|
||||
set color8 { 1.0 0.0 0.0 }
|
||||
|
||||
# darkred 1.0
|
||||
set color9 { 0.93 0.0 0.0 }
|
||||
|
||||
if { $colpcnt < 0.19 } {
|
||||
set nc [lerpcolor $color0 $color1 [expr $colpcnt/(0.19-0.0)]]
|
||||
} elseif { $colpcnt < 0.34 } {
|
||||
set nc [lerpcolor $color1 $color2 [expr ($colpcnt-0.19)/(0.34-0.19)]]
|
||||
} elseif { $colpcnt < 0.4001 } {
|
||||
set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.34)/(0.4001-0.34)]]
|
||||
} elseif { $colpcnt < 0.445 } {
|
||||
set nc [lerpcolor $color2 $color3 [expr ($colpcnt-0.4001)/(0.445-0.4001)]]
|
||||
} elseif { $colpcnt < 0.535 } {
|
||||
set nc [lerpcolor $color3 $color4 [expr ($colpcnt-0.445)/(0.535-0.445)]]
|
||||
} elseif { $colpcnt < 0.69 } {
|
||||
set nc [lerpcolor $color4 $color5 [expr ($colpcnt-0.535)/(0.69-0.535)]]
|
||||
} elseif { $colpcnt < 0.73} {
|
||||
set nc [lerpcolor $color5 $color6 [expr ($colpcnt-0.69)/(0.73-0.69)]]
|
||||
} elseif { $colpcnt < 0.755} {
|
||||
set nc [lerpcolor $color6 $color7 [expr ($colpcnt-0.73)/(0.755-0.73)]]
|
||||
} else {
|
||||
set nc [lerpcolor $color7 $color8 [expr ($colpcnt-0.755)/(1.0-0.755)]]
|
||||
}
|
||||
|
||||
# set nc [coltogs $nc]
|
||||
foreach {r g b} $nc {}
|
||||
puts "index: $i $r $g $b -- $colpcnt"
|
||||
display update ui
|
||||
color change rgb $i $r $g $b
|
||||
}
|
||||
display update on
|
||||
}
|
||||
|
||||
jet_tricolor_scale
|
||||
|
||||
@ -1,19 +0,0 @@
|
||||
# First, rescale and interpolate the positions
|
||||
# where the monomers will be located. (This step is not needed
|
||||
# if the coords_orig.raw file already has correct coordinates.)
|
||||
# The first argument, 32768 is the number of atoms in the desired file.
|
||||
# The second argument, 1.6198059 = 4.25^(1/3), tells interpolate_coords.py
|
||||
# to multiply all the coordinates (scale them up) by 1.6198059.
|
||||
|
||||
./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw
|
||||
|
||||
# Then, build the "system.lt" file
|
||||
|
||||
./generate_system_lt.py 32768 51 < coords.raw > system.lt
|
||||
|
||||
# 32768 is the number of monomers in the polymer
|
||||
# (which may be different from the number of coordinates
|
||||
# in the "coords_orig.raw" file) This number will vary
|
||||
# depending on how long you want the polymer to be.
|
||||
# The second argument "51" is the average interval between
|
||||
# condensin anchors (IE the "loop size" in monomers.)
|
||||
@ -1,57 +0,0 @@
|
||||
---- Andrew's comments ----
|
||||
|
||||
The two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.
|
||||
|
||||
For the 10nm model,
|
||||
n=128000,
|
||||
L=200,
|
||||
U(alpha)=5*(1 - cos(alpha))
|
||||
bond_length=1.0 (=10nm)
|
||||
sigma=1.0 (particle radius = 10nm)
|
||||
|
||||
30nm-fiber model details:
|
||||
"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."
|
||||
|
||||
I interpret this to mean that, for the 30nm model,
|
||||
n=128000/4.25~=30117
|
||||
L=200/4.25~=47
|
||||
U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647)
|
||||
To increase the volume by a factor o 4.25, originally I thought I should increase the "sigma" parameter from 1.0 to 4.25^(1/3)~=1.6198. But I suspect that the bond-lengths between monomers should be fixed at 1.0. If that is the case, then, perhaps I should increase "sigma" from 1.0 to 4.25^(1/2)~=2.061552, and keep the bond-length fixed at 1.0 (which in the units used by thsi paper, corresponds to 10nm). (That would increase the volume of a cylinder of radius "sigma" and length="bond-length" by a factor of 4.25)
|
||||
bond_length=1.0 (10nm again)
|
||||
sigma=2.061552 (Yes, this is less than 3.0<-->30nm. See below.)
|
||||
|
||||
|
||||
|
||||
|
||||
--- Excerpts from the Supplemental section of Naumova et al Science 2013 ---
|
||||
|
||||
From p. 18 of the supplemental materials section of Naumova et al Science 2013.
|
||||
|
||||
(This section was probably written by Maxim Imakaev.)
|
||||
|
||||
In vivo, the structure of the chromatin fiber can be complicated and many details remain unknown, particularly in metaphase. Given this uncertainty, we simulated chromatin as a homogeneous “beads-on-a-string” polymer fiber. We consider a 10nm fiber, as the pervasiveness of the 30nm fiber in vivo has become increasingly contested. In our simulations, 77Mb is represented by a densely-packed 10nm fiber of 128,000 monomers. Each monomer represents a 10nm-sized DNA-histone complex containing 3 nucleosomes (around 600bp). The fiber has a persistence length of 4 monomers (~2.4Kb), which is based on earlier estimates of 5-10 nucleosomes for interphase (14). Those estimates arise from the assumption that 5-10 linker DNA fragments, each of 20-40bp, can collectively provide flexibility equal to that of the 150bp persistence length of DNA. Binding of proteins to the linker DNA (e.g. histone H1) and interactions between neighboring nucleosomes can further constrain dynamics, requiring more linkers to provide the persistence length. Due to the tight packing of nucleosomes in metaphase, we use the upper limit of this range, i.e. 12 nucleosomes.
|
||||
For the consecutive loops on a scaffold model (the final folded state model with the best agreement with Hi-C data), we also performed simulations with a more flexible 10nm fiber, or with a 30nm fiber, and found similar results. The more flexible 10nm fiber was modeled by decreasing persistence length to 1.8 monomers. The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level. We note that a classic model of a 30nm fiber is much less dense than a compact metaphase chromosome. A textbook model of a 30nm fiber assumes packing of about 6 nucleosomes per 10nm of fiber length. This model predicts that only 28% of the volume of the fiber (a 30nm-diameter cylinder) is occupied by nucleosomes, assuming a nucleosome shell volume of 328 nm^3. This is much less than the estimated 30-50% density of nucleosomes in a metaphase chromosome, assuming a diameter of 600nm, a packing density of 50-70 Mb/um, and the same nucleosome volume. (See also (15), which gives an estimate of 0.14-0.18 pg/μm for DNA only, and would give about twice the density if DNA is counted with nucleosomes). As follows, these fibers would have to interdigitate, and fill in gaps within each other. We account for this overlap by assuming the effective diameter of the fiber to be less than 30nm. The effective diameter was chosen to make the volume of the fiber equal the total volume of all the nucleosomes.
|
||||
|
||||
We accounted for topoisomerase II activity by allowing chromatin fibers to pass through each other, while still having excluded volume interactions. This was achieved by using a soft-core Lennard-Jones potential with 1kT energy cost for monomer overlap (see below). This allows for changes in the topological state of a chromosome that are known to occur during compaction in vivo.
|
||||
|
||||
Our simulations of a two-step folding process show that Hi-C data for mitotic chromosomes is consistent with a linearly compressed array of consecutive chromatin loops. Whereas mechanisms for formation of consecutive chromatin loops have been proposed, the process of axial compression is less understood. Chromatid compression cannot be accomplished by increased chromatin-chromatin affinity alone, as this would lead to condensation into a globular geometry (14, 16, 17). However, mechanisms which locally compress the fiber of loop bases naturally allow for anisotropic compression into a shorter and thicker fiber, with the same width regardless of chromosome length (18). Differences in the duration or efficiency of the first and second stages of chromosomal condensation provide a natural mechanism for condensation-related proteins to separately affect mitotic chromosome length and width (19). We also note that the axis of loop-bases in our two-stage model does not necessarily form a continuous and rigid scaffold (Figure S26). As follows, we remain agnostic about the molecular details of the chromosomal scaffold, which might for example be formed by a network consisting of protein-protein and/or protein-DNA interactions (20).
|
||||
|
||||
1. Polymer simulations
|
||||
|
||||
To perform Langevin dynamics polymer simulations we used OpenMM, a high-performance GPU-assisted molecular dynamics API (21, 22). To represent chromatin fibers as polymers, we used a sequence of spherical monomers of 1 unit of length in diameter. Here and below all distances are measured in monomer sizes, set to be 10nm unless specified otherwise. Neighboring monomers are connected by harmonic bonds, with a potential U = 100*(r - 1)^2 (here and below in units of kT). Polymer stiffness is modeled with a three point interaction term, with the potential U = 5*(1 - cos(alpha)), where alpha is the angle between neighboring bonds. All monomers interact via either a shifted Lennard-Jones (LJ) repulsive potential, or an attractive Lennard-Jones potential. At high densities in a confined volume, the details of the inter-monomer interactions become negligible due to screening (23), and we therefore used the computationally efficient shifted LJ potential. The shifted LJ potential allows for a short-range repulsion by truncating the LJ potential at its minimum and shifting the minimum to zero: U = 4 * (1/r^12 - 1/r^6) + 1, for r<2^(1/6); U=0 for r > 2^(1/6). The shifted LJ potential is one of the most computationally efficient repulsive potentials due to a very short cutoff radius.
|
||||
|
||||
To allow chain passing, which represents activity of topoisomerase II, we softened the shifted LJ potential by truncating the interaction energy at Ecutoff = 1 kT. At energies more than 0.5 Ecutoff, the LJ potential was softened via: Usoftened = 0.5 * Ecutoff * (1 + tanh(2*U/Ecutoff - 1)). To avoid numerical 19instabilities in the calculation of U at r ~ 0, the interaction radius r was truncated at r=0.3 via: rtruncated = (r^10 + (0.3)^10)^0.1, which introduced negligible shift in a final softened potential. For an attractive LJ potential, we used: U = 4 * e * (1/r^12 - 1/r^6), with e = 0.46 kT, slightly below the theta-temperature. The attractive potential was similarly softened at 2 kT and cut off at r=2.5. Unless noted, we used a softened shifted LJ repulsive potential.
|
||||
|
||||
Polymer models were visualized using Pymol and Rasmol. For images with loop bases highlighted, a base of each loop and 3 monomers surrounding it in each direction were labeled in red.
|
||||
|
||||
SECTIONS 2-5 SKIPPED
|
||||
|
||||
6. Two-stage process: linear compaction - axial compression
|
||||
|
||||
To simulate the two-stage process of metaphase chromosome folding, we used the 30nm fiber representation described above for its computational efficiency. Simulations were initialized from 30000 monomer fractal globule conformations; fractal globule is a model for interphase chromatin organization. First, random consecutive loops with L=100 monomers (see above) were introduced, and anchors of neighboring loops were brought together using harmonic springs with a potential U = k * (r – r0)2; r0=0.5. To avoid abrupt motion of the loop anchors, the force was gradually turned on over the first
|
||||
300000 timesteps, with k linearly increasing in time from 0 to 10 kT. We used softened shifted repulsive LJ potential for inter-monomer interaction.
|
||||
|
||||
Upon completion of linear compaction, axial compression was initiated. This involves following changes: the repulsive LJ force is replaced with an attractive LJ force for all monomers, and the chromosomal core of loop anchors is homogeneously compressed. To achieve the latter, all anchor pairs separated by less than 30 anchors were attracted via a potential U = step(d-3) * abs(d-3) * 10 kT, which implements a constant attractive force between two anchors if they are separated by a distance larger than 3. The interactions between neighboring loop anchors were kept throughout this process.
|
||||
|
||||
To obtain the contact map from this simulation, 50 independent runs of 1.5e7 timesteps were performed, and 250 conformations were collected from the second half of each run. The contact map was calculated from all conformations of all runs at a 30-monomer resolution, and was further averaged over three 10000-monomer blocks along the diagonal of the heatmap. The latter was done to show contact map at a relevant length scale (0 to 25 Mb), and to achieve a better averaging of the contact map.
|
||||
|
||||
@ -1,8 +0,0 @@
|
||||
|
||||
|
||||
for ((i=0; i<60; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` 0 0; done
|
||||
|
||||
echo 61 3.0 0 -5
|
||||
|
||||
for ((i=61; i<=4000; i++)); do echo "$((i+1)) " `echo "$i*0.05" | bc` `echo "($i-60)*0.5"|bc` -10; done
|
||||
|
||||
@ -1,47 +0,0 @@
|
||||
# This file contains the definition of a molecule named "CondensinMonomer".
|
||||
# (This particular molecule contain only one atom, but that is up to you.)
|
||||
# Later, multiple CondensinMonomers can be connected together to build a molecule.
|
||||
|
||||
|
||||
|
||||
CondensinMonomer {
|
||||
|
||||
# atom-id mol-id(ignore) atom-type q x y z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000
|
||||
}
|
||||
|
||||
# (The x y z positions will be changed later with move commands
|
||||
# You can spedify charge and other properties by changing the atom_style.)
|
||||
|
||||
|
||||
|
||||
# atom-type mass
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:A 1.0
|
||||
}
|
||||
|
||||
# pairwise interactions (between non-bonded atoms):
|
||||
#
|
||||
# U(r) = 4*eps*((r/sig)^12 - (r/sig)^6)
|
||||
#
|
||||
# Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0
|
||||
#
|
||||
# atom-type atom-type pair_style epsilon sigma
|
||||
|
||||
write_once("In Settings") {
|
||||
# I usually use sigma = 2^(-(1/6)), with a cutoff of 1
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0
|
||||
# In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0
|
||||
# with a cutoff of 2^(1/6). Here we are trying to reproduce his results.
|
||||
# 10nm fiber
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373
|
||||
# 30nm fiber (4.25^(1/2)=2.0615528128088303)
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349
|
||||
# 30nm fiber (4.25^(1/3)=1.6198059006387417)
|
||||
pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708
|
||||
}
|
||||
|
||||
} # CondensinMonomer
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,301 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
err_msg = """
|
||||
Usage:
|
||||
|
||||
generate_system_lt.py n < monomer_coords.raw > system.lt
|
||||
|
||||
Example:
|
||||
|
||||
generate_system_lt.py 30118 47 < coords.raw > system.lt
|
||||
|
||||
Explanation:
|
||||
ARGUMENTS:
|
||||
n = total length of the polymer (in monomers)
|
||||
L = the (average) length of each condensin interval (Poisson-
|
||||
distributed) This is also 1/probability that each monomer
|
||||
is a "condensin monomer".
|
||||
|
||||
(Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner,
|
||||
and 47 = 200/4.25. Note that 128000 and 200 are for the 10nm model.
|
||||
See the supplemental section of Naumova et al Science 2013, p 18.)
|
||||
|
||||
"""
|
||||
|
||||
|
||||
import sys
|
||||
import random
|
||||
from math import *
|
||||
|
||||
# Parse the argument list:
|
||||
if len(sys.argv) <= 2:
|
||||
sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n")
|
||||
exit(1)
|
||||
N=int(sys.argv[1])
|
||||
L=float(sys.argv[2])
|
||||
if len(sys.argv) > 3:
|
||||
delta_x = float(sys.argv[3])
|
||||
else:
|
||||
delta_x = 2.0
|
||||
if len(sys.argv) > 4:
|
||||
x_offset = float(sys.argv[4])
|
||||
else:
|
||||
x_offset = -((N-1.0)/2) * delta_x
|
||||
|
||||
|
||||
coords = [[0.0, 0.0, 0.0] for i in range(0,N)]
|
||||
lines = sys.stdin.readlines()
|
||||
if len(lines) != N:
|
||||
sys.stderr.write("Error: Number of lines in input file ("+str(len(lines))+")\n"
|
||||
" does not match first argument ("+str(N)+")\n")
|
||||
exit(1)
|
||||
for i in range(0, N):
|
||||
coords[i] = map(float, lines[i].split())
|
||||
|
||||
# Now calculate the box_boundaries:
|
||||
box_bounds_min = [0.0, 0.0, 0.0]
|
||||
box_bounds_max = [0.0, 0.0, 0.0]
|
||||
for i in range(0, N):
|
||||
for d in range(0, 3):
|
||||
if i == 0:
|
||||
box_bounds_min[d] = coords[i][d]
|
||||
box_bounds_max[d] = coords[i][d]
|
||||
else:
|
||||
if coords[i][d] > box_bounds_max[d]:
|
||||
box_bounds_max[d] = coords[i][d]
|
||||
if coords[i][d] < box_bounds_min[d]:
|
||||
box_bounds_min[d] = coords[i][d]
|
||||
|
||||
# Now scale the box boundaries outward by 50%
|
||||
box_scale = 1.5
|
||||
for d in range(0,3):
|
||||
box_bounds_cen = 0.5*(box_bounds_max[d] + box_bounds_min[d])
|
||||
box_bounds_width = box_bounds_max[d] - box_bounds_min[d]
|
||||
box_bounds_min[d] = box_bounds_cen - 0.5*box_scale*box_bounds_width
|
||||
box_bounds_max[d] = box_bounds_cen + 0.5*box_scale*box_bounds_width
|
||||
|
||||
# Now calculate the direction each molecule should be pointing at:
|
||||
direction_vects = [[0.0, 0.0, 0.0] for i in range(0,N)]
|
||||
for d in range(0, 3):
|
||||
direction_vects[0][d] = coords[1][d] - coords[0][d]
|
||||
direction_vects[N-1][d] = coords[N-1][d] - coords[N-2][d]
|
||||
for i in range(1, N-1):
|
||||
for d in range(0, 3):
|
||||
direction_vects[i][d] = coords[i+1][d] - coords[i-1][d]
|
||||
|
||||
# Optional: normalize the direction vectors
|
||||
for i in range(1, N-1):
|
||||
direction_len = 0.0
|
||||
for d in range(0, 3):
|
||||
direction_len += (direction_vects[i][d])**2
|
||||
direction_len = sqrt(direction_len)
|
||||
for d in range(0, 3):
|
||||
direction_vects[i][d] /= direction_len
|
||||
|
||||
# Now, begin writing the text for the system.lt file:
|
||||
|
||||
sys.stdout.write(
|
||||
"""
|
||||
import "monomer.lt" # <-- defines "Monomer"
|
||||
import "condensin.lt" # <-- defines "CondensinMonomer"
|
||||
|
||||
|
||||
"""
|
||||
)
|
||||
|
||||
|
||||
|
||||
# Figure out which monomers are "Monomers" and which monomers are
|
||||
# "CondensinMonomers"
|
||||
|
||||
ic = 0 # count the number of condensins added so far
|
||||
condensin_is_here = [False for i in range(0, N)]
|
||||
for i in range(0, N):
|
||||
#add_condensin_here = random.random() < (1.0 / L)
|
||||
add_condensin_here = random.random() < (1.0 / (L-2.0))
|
||||
|
||||
# We do not allow condensin at successive sites separated by less than 2
|
||||
# subunits (the "L-2.0" above is to compensate for this)
|
||||
if (((i > 0) and condensin_is_here[i-1]) or
|
||||
((i > 1) and condensin_is_here[i-2])):
|
||||
add_condensin_here = False
|
||||
|
||||
if add_condensin_here:
|
||||
condensin_is_here[i] = True
|
||||
ic += 1
|
||||
Nc = ic
|
||||
|
||||
|
||||
ic = 0
|
||||
for i in range(0, N):
|
||||
if condensin_is_here[i]:
|
||||
sys.stdout.write("condensins["+str(ic)+"] = new CondensinMonomer.scale(0.5,0.8,0.8).rotvv(1,0,0,")
|
||||
ic+=1
|
||||
else:
|
||||
sys.stdout.write("monomers["+str(i)+"] = new Monomer.scale(0.5,0.8,0.8).rotvv(1,0,0,")
|
||||
sys.stdout.write(str(direction_vects[i][0])+","
|
||||
+str(direction_vects[i][1])+","
|
||||
+str(direction_vects[i][2])+
|
||||
").move("
|
||||
+str(coords[i][0])+","
|
||||
+str(coords[i][1])+","
|
||||
+str(coords[i][2])+")\n")
|
||||
|
||||
#if condensin_is_here[i]:
|
||||
# if i < N-1:
|
||||
# sys.stdout.write("\n"
|
||||
# "#(override the dihedral angle for this monomer)\n"
|
||||
# "write(\"Data Dihedrals\") {\n"
|
||||
# " $dihedral:twistor"+str(i+1)+" @dihedral:CondensinMonomer/TWISTOR $atom:monomers["+str(i)+"]/t $atom:monomers["+str(i)+"]/c $atom:monomers["+str(i+1)+"]/c $atom:monomers["+str(i+1)+"]/t\n"
|
||||
# "}\n"
|
||||
# "\n")
|
||||
|
||||
|
||||
|
||||
sys.stdout.write(
|
||||
"""
|
||||
|
||||
# ---------------- simulation box -----------------
|
||||
|
||||
# Now define a box big enough to hold a polymer with this (initial) shape
|
||||
|
||||
"""
|
||||
)
|
||||
|
||||
|
||||
sys.stdout.write("write_once(\"Data Boundary\") {\n"
|
||||
+str(box_bounds_min[0])+" "+str(box_bounds_max[0])+" xlo xhi\n"
|
||||
+str(box_bounds_min[1])+" "+str(box_bounds_max[1])+" ylo yhi\n"
|
||||
+str(box_bounds_min[2])+" "+str(box_bounds_max[2])+" zlo zhi\n"
|
||||
"}\n\n\n")
|
||||
|
||||
|
||||
sys.stdout.write(
|
||||
"""
|
||||
# What kind of boundary conditions are we using?
|
||||
|
||||
write_once("In Init") {
|
||||
boundary s s s # <-- boundary conditions in x y z directions
|
||||
#boundary p p p # <-- boundary conditions in x y z directions
|
||||
}
|
||||
# "p" stands for "periodic"
|
||||
# "s" stands for "shrink-wrapped" (non-periodic)
|
||||
|
||||
|
||||
# ---- Bonds ----
|
||||
|
||||
|
||||
write_once("In Settings") {
|
||||
# 10nm model:
|
||||
#bond_coeff @bond:backbone harmonic 100.0 1.0
|
||||
# 30nm fiber (4.25^(1/3)=1.6198059006387417)
|
||||
bond_coeff @bond:backbone harmonic 100.0 1.6198059006387417
|
||||
}
|
||||
|
||||
|
||||
"""
|
||||
)
|
||||
|
||||
|
||||
sys.stdout.write("write(\"Data Bonds\") {\n")
|
||||
|
||||
# Old bond-loop was simple:
|
||||
#for i in range(0, N-1):
|
||||
# sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a $atom:monomers["+str(i+1)+"]/a\n")
|
||||
|
||||
ic = 0
|
||||
for i in range(0, N-1):
|
||||
#sys.stderr.write("i="+str(i)+", ic="+str(ic)+", Nc="+str(Nc)+"\n")
|
||||
|
||||
# Figure out if the first atom in the bond pair
|
||||
# belongs to a regular Monomer or a CondensinMonomer
|
||||
if condensin_is_here[i]:
|
||||
sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:condensins["+str(ic)+"]/a")
|
||||
ic+=1
|
||||
else:
|
||||
sys.stdout.write(" $bond:b"+str(i+1)+" @bond:backbone $atom:monomers["+str(i)+"]/a")
|
||||
|
||||
# Do the same thing for the second atom in the bond pair
|
||||
if condensin_is_here[i+1]:
|
||||
assert(ic<Nc)
|
||||
sys.stdout.write(" $atom:condensins["+str(ic)+"]/a\n")
|
||||
else:
|
||||
sys.stdout.write(" $atom:monomers["+str(i+1)+"]/a\n")
|
||||
|
||||
sys.stdout.write("}\n\n\n")
|
||||
|
||||
|
||||
sys.stdout.write("""
|
||||
|
||||
write_once("Data Angles By Type") {
|
||||
@angle:backbone @atom:* @atom:* @atom:* @bond:backbone @bond:backbone
|
||||
}
|
||||
|
||||
write_once("In Settings") {
|
||||
# Most parameters here were taken from the supplemental material of
|
||||
# Naumova et al. Science 2013 (simulations by Maxim Imakaev, see Supp Mat)
|
||||
#angle_coeff @angle:backbone cosine 5.0 #<-10nm fiber
|
||||
angle_coeff @angle:backbone cosine 1.1764705882352942 #<-30nm fiber
|
||||
}
|
||||
|
||||
""")
|
||||
|
||||
|
||||
sys.stdout.write(
|
||||
"""
|
||||
|
||||
# ---- Condensins randomly located on the polymer ----
|
||||
|
||||
# Stage 1:
|
||||
# Add bonds between consecutive condensin anchors.
|
||||
# Imakaev calls this "stage 1: linear compaction":
|
||||
|
||||
"""
|
||||
)
|
||||
|
||||
sys.stdout.write("write(\"Data Bonds\") {\n")
|
||||
ic = 0
|
||||
for i in range(0, N):
|
||||
if condensin_is_here[i]:
|
||||
if (0 < ic):
|
||||
sys.stdout.write(" $bond:bstage1_"+str(ic-1)+" @bond:stage1 $atom:condensins["+str(ic-1)+"]/a $atom:condensins["+str(ic)+"]/a\n")
|
||||
ic += 1
|
||||
|
||||
sys.stdout.write("}\n\n")
|
||||
|
||||
|
||||
|
||||
sys.stdout.write("""
|
||||
|
||||
# Stage 2:
|
||||
# Add additional bonds between all pairs of condensin anchors
|
||||
# in a window of |ic-jc| <= 30 anchors (along the chain).
|
||||
# In the paper, they call this stage 2 axial compression.
|
||||
|
||||
write("Data Bonds") {
|
||||
""")
|
||||
|
||||
jcwindowsize = 30
|
||||
for ic in range(0, Nc):
|
||||
#jcmin = max(ic-jcwindowsize, 0)
|
||||
#jcmax = min(ic+jcwindowsize, Nc-1)
|
||||
jcmax = min(ic+jcwindowsize, Nc-1)
|
||||
for jc in range(ic+2, jcmax+1):
|
||||
sys.stdout.write(" $bond:bstage2_"+str(ic)+"_"+str(jc)+" @bond:stage2 $atom:condensins["+str(ic)+"]/a $atom:condensins["+str(jc)+"]/a\n")
|
||||
|
||||
sys.stdout.write("}\n")
|
||||
|
||||
|
||||
sys.stdout.write("""
|
||||
|
||||
write_once("In Settings") {
|
||||
# stage 1 bonds are initially off
|
||||
bond_coeff @bond:stage1 harmonic 0.0 0.5 # <--(we can override this later)"
|
||||
# stage 2 bonds are initially off
|
||||
bond_coeff @bond:stage2 harmonic 0.0 0.0 # <--(we can override this later)"
|
||||
}
|
||||
|
||||
""")
|
||||
|
||||
sys.stdout.write("\n\n# "+str(Nc)+" condensin molecules added\n\n")
|
||||
sys.stderr.write("\n\n# "+str(Nc)+" condensin molecules added\n\n")
|
||||
@ -1,74 +0,0 @@
|
||||
#!/usr/bin/env python
|
||||
|
||||
|
||||
err_msg = """
|
||||
Usage:
|
||||
|
||||
interpolate_coords.py Ndesired [scale] < coords_orig.raw > coords.raw
|
||||
|
||||
Example:
|
||||
|
||||
interpolate_coords.py 30118 3.0 < coords_orig.raw > coords.raw
|
||||
|
||||
# (Note: 30117 ~= 128000/4.25, but using 30118 makes interpolation cleaner.
|
||||
# See the supplemental section of Naumova et al Science 2013, p 18.)
|
||||
|
||||
"""
|
||||
|
||||
|
||||
import sys
|
||||
from math import *
|
||||
|
||||
# Parse the argument list:
|
||||
if len(sys.argv) <= 1:
|
||||
sys.stderr.write("Error:\n\nTypical Usage:\n\n"+err_msg+"\n")
|
||||
exit(1)
|
||||
|
||||
n_new = int(sys.argv[1])
|
||||
|
||||
if len(sys.argv) > 2:
|
||||
scale = float(sys.argv[2])
|
||||
else:
|
||||
scale = 1.0
|
||||
|
||||
coords_orig = []
|
||||
|
||||
lines = sys.stdin.readlines()
|
||||
|
||||
for line in lines:
|
||||
tokens = line.split()
|
||||
if (len(tokens) > 0):
|
||||
coords_orig.append(map(float, tokens))
|
||||
g_dim = len(tokens)
|
||||
|
||||
n_orig = len(coords_orig)
|
||||
|
||||
if n_orig < 2:
|
||||
sys.stderr.write("Error:\n\nInput file contains less than two lines of coordinates\n")
|
||||
exit(1)
|
||||
|
||||
if n_new < 2:
|
||||
sys.stderr.write("Error:\n\nOutput file will contain less than two lines of coordinates\n")
|
||||
exit(1)
|
||||
|
||||
coords_new = [[0.0 for d in range(0, g_dim)] for i in range(0, n_new)]
|
||||
|
||||
for i_new in range(0, n_new):
|
||||
I_orig = (i_new) * (float(n_orig-1) / float(n_new-1))
|
||||
i_orig = int(floor(I_orig))
|
||||
i_remainder = I_orig - i_orig
|
||||
|
||||
if (i_new < n_new-1):
|
||||
for d in range(0, g_dim):
|
||||
coords_new[i_new][d] = scale*(coords_orig[i_orig][d]
|
||||
+
|
||||
i_remainder*(coords_orig[i_orig+1][d]-
|
||||
coords_orig[i_orig][d]))
|
||||
else:
|
||||
for d in range(0, g_dim):
|
||||
coords_new[i_new][d] = scale*coords_orig[n_orig-1][d]
|
||||
|
||||
# print the coordates
|
||||
for d in range(0, g_dim-1):
|
||||
sys.stdout.write(str(coords_new[i_new][d]) + ' ')
|
||||
sys.stdout.write(str(coords_new[i_new][g_dim-1]) + "\n")
|
||||
@ -1,84 +0,0 @@
|
||||
# This file contains the definition of a molecule named "Monomer".
|
||||
# (This particular molecule contain only one atom, but that is up to you.)
|
||||
# Later, multiple monomers can be connected together to build a molecule.
|
||||
|
||||
|
||||
|
||||
Monomer {
|
||||
|
||||
# atom-id mol-id(ignore) atom-type q x y z
|
||||
|
||||
write("Data Atoms") {
|
||||
$atom:a $mol @atom:A 0.000 0.00000 0.00000 0.00000
|
||||
}
|
||||
|
||||
# (The x y z positions will be changed later with move commands
|
||||
# You can spedify charge and other properties by changing the atom_style.)
|
||||
|
||||
|
||||
|
||||
# atom-type mass
|
||||
|
||||
write_once("Data Masses") {
|
||||
@atom:A 1.0
|
||||
}
|
||||
|
||||
# pairwise interactions (between non-bonded atoms):
|
||||
#
|
||||
# U(r) = 4*eps*((r/sig)^12 - (r/sig)^6)
|
||||
#
|
||||
# Note: when sigma=0.8908987181403393=2^(1/6), the minimia is at r=1.0
|
||||
#
|
||||
# atom-type atom-type pair_style epsilon sigma rcutoff
|
||||
|
||||
write_once("In Settings") {
|
||||
# I usually use sigma = 2^(-(1/6)), with a cutoff of 1
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 0.8908987181403393 1.0
|
||||
# In the 2013 Science (metaphase) paper, Imakaev used sigma=1.0
|
||||
# with a cutoff of 2^(1/6). Here we are trying to reproduce his results.
|
||||
# 10nm fiber
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 1.0 1.122462048309373
|
||||
# 30nm fiber (4.25^(1/2)=2.0615528128088303)
|
||||
#pair_coeff @atom:A @atom:A lj/cut 1.0 2.0615528128088303 2.314014792963349
|
||||
# 30nm fiber (4.25^(1/3)=1.6198059006387417)
|
||||
pair_coeff @atom:A @atom:A lj/cut 1.0 1.6198059006387417 1.8181706490945708
|
||||
}
|
||||
|
||||
} # Monomer
|
||||
|
||||
|
||||
|
||||
|
||||
# --------------------------------------------------------------------
|
||||
#
|
||||
# At some point we need to specify which force-field styles we want.
|
||||
# LAMMPS also allows you to customize the kinds of properties you want
|
||||
# each atom to have (the "atom_style"), such as charge, molecule-id, dipole etc.
|
||||
# I typically specify this here. Doing it this way means that all systems built
|
||||
# from "Monomers" (ie which import "monomer.lt") share these atom-styles
|
||||
# and force-field styles by default. You can override these settings later.
|
||||
|
||||
|
||||
write_once("In Init") {
|
||||
# Default styles for molecules built out of "Monomers"
|
||||
units lj
|
||||
atom_style full
|
||||
|
||||
bond_style hybrid harmonic table linear 4001
|
||||
angle_style hybrid cosine
|
||||
dihedral_style none
|
||||
|
||||
# If you need angles, dihedrals and impropers, uncomment or replace:
|
||||
# angle_style hybrid harmonic
|
||||
# dihedral_style hybrid fourier
|
||||
|
||||
pair_style hybrid lj/cut 2.5
|
||||
|
||||
# If you are using gpu acceleration uncomment these lines:
|
||||
# package gpu force/neigh 0 0 1.0
|
||||
# pair_style hybrid lj/cut/gpu 4.0
|
||||
|
||||
pair_modify mix arithmetic
|
||||
special_bonds lj/coul 1 1 1
|
||||
}
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1,41 +0,0 @@
|
||||
#########################################################
|
||||
# Example how to run this file:
|
||||
#
|
||||
# 1) Choose a ransom seed (in this case 141203)
|
||||
# (or use `bash -c 'echo $RANDOM'`)
|
||||
#
|
||||
# 2) Then, from the shell, invoke LAMMPS to collapse the polymer:
|
||||
#
|
||||
# lmp_ubuntu_parallel -i run.in -var seed 141203
|
||||
#
|
||||
#########################################################
|
||||
# eg:
|
||||
# time mpirun -np 2 lmp_ubuntu_parallel -i run.in.min
|
||||
#########################################################
|
||||
|
||||
# -- 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 10000 traj_min.lammpstrj id mol type x y z ix iy iz
|
||||
thermo_style custom step pe etotal vol epair ebond eangle edihed
|
||||
thermo_modify norm no #(report total energy not energy / num_atoms)
|
||||
thermo 100 #(time interval for printing out "thermo" data)
|
||||
|
||||
# Now minimize the system:
|
||||
|
||||
min_style quickmin
|
||||
min_modify dmax 0.05
|
||||
minimize 1.0e-7 1.0e-8 30000 100000000
|
||||
|
||||
write_data system_after_min.data
|
||||
@ -1,110 +0,0 @@
|
||||
# PREREQUISITES: You must run LAMMPS using "run.in.min" beforehand.
|
||||
# (This will create the "system_after_min0.data" file needed below.)
|
||||
#########################################################
|
||||
# Run using:
|
||||
#
|
||||
# lmp_ubuntu_parallel -i run.in.stage1
|
||||
#
|
||||
#########################################################
|
||||
# GPUs:
|
||||
# To enable gpu acceleration, make sure settings.in.init includes this line:
|
||||
# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.)
|
||||
# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings"
|
||||
# files with "lj/cut/gpu"
|
||||
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
#read_data system.data
|
||||
read_data system_after_min.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
# DON'T MINIMIZE FIRST UNLESS YOU CHOOSE THE CORRECT INITIAL KbondC FORMULA
|
||||
#thermo_style custom step pe etotal vol epair ebond eangle edihed
|
||||
#thermo_modify norm no #(report total energy not energy / num_atoms)
|
||||
#thermo 20 #(time interval for printing out "thermo" data)
|
||||
#min_style sd
|
||||
#min_modify dmax 0.05
|
||||
#minimize 1.0e-7 1.0e-8 20000 1000000
|
||||
#write_data system_after_min_t=0.data
|
||||
|
||||
|
||||
mass * 1.0
|
||||
timestep 0.005 # "dt"
|
||||
dump 1 all custom 25000 traj_stage1.lammpstrj id mol type x y z ix iy iz
|
||||
reset_timestep 0
|
||||
|
||||
|
||||
# --- run the simulation ---
|
||||
|
||||
|
||||
# set the velocity to zero
|
||||
velocity all create 0.0 123456
|
||||
|
||||
# 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.)
|
||||
|
||||
# Tstart Tstop tdamp randomseed
|
||||
|
||||
fix fxlan all langevin 1.0 1.0 10.0 123456
|
||||
|
||||
# pstart pstop pdamp(time-units, 2000 iters usually)
|
||||
#fix fxnph all nph x -0.000 -0.000 1.0
|
||||
fix fxnve all nve
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html)
|
||||
|
||||
fix fxcenter all recenter 0.0 0.0 0.0
|
||||
|
||||
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 1000 #(time interval for printing out "thermo" data)
|
||||
|
||||
#balance dynamic x 20 1.0 -out tmp.balance
|
||||
#balance x uniform
|
||||
|
||||
|
||||
variable nloop1 loop 300
|
||||
|
||||
label loop1
|
||||
|
||||
print "############### LOOP ${nloop1} ###############"
|
||||
|
||||
# Now, change the bond-strength between condensin monomers.
|
||||
# From the Naumova et al Science 2013 paper (supp materials)
|
||||
# "Two-stage model: linear compaction + axial compression"
|
||||
# "First, random consecutive loops with L=100 monomers (see above) were
|
||||
# introduced, and anchors of neighboring loops were brought together
|
||||
# using harmonic springs with a potential U = k * (r – r0)2; r0=0.5.
|
||||
# To avoid abrupt motion of the loop anchors, the force was gradually
|
||||
# turned on over the first 300000 timesteps, with k linearly increasing
|
||||
# in time from 0 to 10 kT."
|
||||
# Do this by changing the parameters in the force-field for these
|
||||
# bonds.
|
||||
#
|
||||
# Formula used for "bond_style harmonic":
|
||||
# Ubond(r) = k*(r-r0)^2
|
||||
# bondType style
|
||||
#bond_coeff 1 harmonic 0.1 0.5
|
||||
|
||||
variable time equal step
|
||||
variable KbondC equal $((v_time+1)*(10.0/300000.0))
|
||||
print "timestep = ${time}, KbondC = ${KbondC}" file KbondC_vs_time.dat
|
||||
|
||||
#bond_coeff 1 harmonic ${KbondC} 0.5
|
||||
bond_coeff 1 harmonic ${KbondC} 0.5
|
||||
run 1000
|
||||
|
||||
next nloop1
|
||||
jump SELF loop1
|
||||
|
||||
write_data system_after_stage1.data
|
||||
|
||||
@ -1,90 +0,0 @@
|
||||
# PREREQUISITES: You must run LAMMPS using "run.in.stage1" beforehand.
|
||||
# (This will create the "system_after_stage1.data" file.)
|
||||
#########################################################
|
||||
# Run using:
|
||||
#
|
||||
# lmp_ubuntu_parallel -i run.in.stage2
|
||||
#
|
||||
#########################################################
|
||||
# eg:
|
||||
# time mpirun -np 2 lmp_ubuntu_parallel -i run.in -var seed 1
|
||||
#########################################################
|
||||
# GPUs:
|
||||
# To enable gpu acceleration, make sure settings.in.init includes this line:
|
||||
# package gpu force/neigh 0 0 1.0 (make sure it is not commented out.)
|
||||
# ...and replace "lj/cut" in the "settings.in.init" and "settings.in.settings"
|
||||
# files with "lj/cut/gpu"
|
||||
|
||||
|
||||
# -- Init Section --
|
||||
|
||||
include system.in.init
|
||||
|
||||
# -- Atom Definition Section --
|
||||
|
||||
#read_data system.data
|
||||
read_data system_after_stage1.data
|
||||
|
||||
# -- Settings Section --
|
||||
|
||||
include system.in.settings
|
||||
|
||||
# -- Run Section --
|
||||
|
||||
|
||||
mass * 1.0
|
||||
timestep 0.005 # "dt"
|
||||
dump 1 all custom 50000 traj_stage2.lammpstrj id mol type x y z ix iy iz
|
||||
reset_timestep 300000
|
||||
|
||||
|
||||
# --- run the simulation ---
|
||||
|
||||
# set the velocity to zero
|
||||
velocity all create 0.0 123456
|
||||
|
||||
# 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.)
|
||||
|
||||
# Tstart Tstop tdamp randomseed
|
||||
|
||||
fix fxlan all langevin 1.0 1.0 10.0 123456
|
||||
|
||||
# pstart pstop pdamp(time-units, 2000 iters usually)
|
||||
fix fxnve all nve
|
||||
# (See http://lammps.sandia.gov/doc/fix_langevin.html)
|
||||
|
||||
fix fxcenter all recenter 0.0 0.0 0.0
|
||||
|
||||
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 1000 #(time interval for printing out "thermo" data)
|
||||
|
||||
#balance dynamic x 20 1.0 -out tmp.balance
|
||||
#balance x uniform
|
||||
|
||||
# atomTypes pairStyle epsilon sigma rcutoff
|
||||
# 10nm-fiber
|
||||
#pair_coeff 1 1 lj/cut 1.0 1.0 2.5
|
||||
#pair_coeff 2 2 lj/cut 1.0 1.0 2.5
|
||||
# 30nm fiber (4.25^(1/3)=1.6198059006387417)
|
||||
pair_coeff 1 1 lj/cut 1.0 1.6198059006387417 4.049514751596854
|
||||
pair_coeff 2 2 lj/cut 1.0 1.6198059006387417 4.049514751596854
|
||||
|
||||
|
||||
# During stage 2, add attractive forces between all pairs of non-consecutive
|
||||
# condensin anchors. These forces are stored in the table file below:
|
||||
# bondType bondStyle filename label
|
||||
bond_coeff 2 table table_bonds_stage2.dat STAGE2
|
||||
|
||||
# During stage 2, I assume the stage-1 bonds remain in place
|
||||
# (They have length 0.5.
|
||||
# After 300000 timesteps during stage 1, the "k" value should be 10.0.)
|
||||
|
||||
# bondType bondStyle k r0
|
||||
bond_coeff 1 harmonic 10.0 0.5
|
||||
|
||||
timestep 0.005
|
||||
run 1700000
|
||||
|
||||
write_data system_after_stage2.data
|
||||
@ -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
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
@ -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 ../
|
||||
@ -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.)
|
||||
@ -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
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 15 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 17 KiB |
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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.
|
||||
@ -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))
|
||||
|
||||
@ -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))
|
||||
|
||||
@ -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)
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -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 -4.56769153408 0.0738800794563
|
||||
25 24.0 -4.64102186743 0.0727680008923
|
||||
26 25.0 -4.71320253365 0.0715809208518
|
||||
27 26.0 -4.78415908407 0.0703199708131
|
||||
28 27.0 -4.85381827903 0.0689864371778
|
||||
29 28.0 -4.92210824234 0.067581760373
|
||||
30 29.0 -4.98895861476 0.0661075335571
|
||||
31 30.0 -5.05430070586 0.0645655009259
|
||||
32 31.0 -5.11806764409 0.0629575556235
|
||||
33 32.0 -5.18019452449 0.061285737258
|
||||
34 33.0 -5.24061855376 0.0595522290273
|
||||
35 34.0 -5.29927919225 0.0577593544584
|
||||
36 35.0 -5.3561182925 0.0559095737673
|
||||
37 36.0 -5.41108023395 0.0540054798439
|
||||
38 37.0 -5.46411205346 0.0520497938726
|
||||
39 38.0 -5.51516357127 0.0500453605949
|
||||
40 39.0 -5.56418751203 0.0479951432253
|
||||
41 40.0 -5.61113962059 0.0459022180302
|
||||
42 41.0 -5.65597877221 0.0437697685824
|
||||
43 42.0 -5.69866707689 0.0416010797029
|
||||
44 43.0 -5.7391699774 0.0393995311046
|
||||
45 44.0 -5.77745634094 0.0371685907508
|
||||
46 45.0 -5.81349854393 0.034911807945
|
||||
47 46.0 -5.84727254977 0.0326328061676
|
||||
48 47.0 -5.87875797937 0.030335275675
|
||||
49 48.0 -5.90793817411 0.0280229658805
|
||||
50 49.0 -5.93480025113 0.0256996775336
|
||||
51 50.0 -5.95933515063 0.0233692547166
|
||||
52 51.0 -5.98153767519 0.0210355766777
|
||||
53 52.0 -6.00140652074 0.0187025495211
|
||||
54 53.0 -6.01894429926 0.016374097773
|
||||
55 54.0 -6.03415755288 0.0140541558448
|
||||
56 55.0 -6.04705675953 0.0117466594146
|
||||
57 56.0 -6.05765632981 0.00945553674764
|
||||
58 57.0 -6.06597459526 0.00718469997761
|
||||
59 58.0 -6.07203378786 0.00493803637051
|
||||
60 59.0 -6.07586001075 0.00271939959245
|
||||
61 60.0 -6.07748320034 0.000532601003776
|
||||
62 61.0 -6.07693707962 -0.00161859899905
|
||||
63 62.0 -6.07425910291 -0.00373049957158
|
||||
64 63.0 -6.06949039207 -0.00579946791801
|
||||
65 64.0 -6.06267566421 -0.00782194767468
|
||||
66 65.0 -6.05386315117 -0.00979446715893
|
||||
67 66.0 -6.04310451074 -0.0117136474624
|
||||
68 67.0 -6.03045472992 -0.0135762103679
|
||||
69 68.0 -6.01597202036 -0.0153789860691
|
||||
70 69.0 -5.99971770618 -0.0171189206741
|
||||
71 70.0 -5.98175610439 -0.0187930834719
|
||||
72 71.0 -5.9621543982 -0.0203986739443
|
||||
73 72.0 -5.9409825034 -0.0219330285036
|
||||
74 73.0 -5.91831292823 -0.0233936269399
|
||||
75 74.0 -5.89422062685 -0.0247780985587
|
||||
76 75.0 -5.86878284696 -0.0260842279959
|
||||
77 76.0 -5.84207897162 -0.0273099606906
|
||||
78 77.0 -5.81419035593 -0.0284534080045
|
||||
79 78.0 -5.78520015867 -0.0295128519729
|
||||
80 79.0 -5.7551931694 -0.0304867496727
|
||||
81 80.0 -5.72425563141 -0.0313737371989
|
||||
82 81.0 -5.6924750609 -0.0321726332348
|
||||
83 82.0 -5.65994006273 -0.0328824422092
|
||||
84 83.0 -5.62674014332 -0.0335023570292
|
||||
85 84.0 -5.59296552097 -0.0340317613814
|
||||
86 85.0 -5.55870693409 -0.0344702315961
|
||||
87 86.0 -5.52405544786 -0.0348175380654
|
||||
88 87.0 -5.48910225957 -0.0350736462148
|
||||
89 88.0 -5.45393850338 -0.0352387170203
|
||||
90 89.0 -5.41865505462 -0.0353131070729
|
||||
91 90.0 -5.38334233438 -0.0352973681855
|
||||
92 91.0 -5.34809011465 -0.0351922465446
|
||||
93 92.0 -5.31298732458 -0.0349986814067
|
||||
94 93.0 -5.27812185824 -0.034717803342
|
||||
95 94.0 -5.24358038438 -0.0343509320285
|
||||
96 95.0 -5.2094481586 -0.0338995736008
|
||||
97 96.0 -5.17580883839 -0.0333654175598
|
||||
98 97.0 -5.14274430152 -0.0327503332496
|
||||
99 98.0 -5.11033446814 -0.0320563659092
|
||||
100 99.0 -5.07865712698 -0.0312857323082
|
||||
101 100.0 -5.04778776623 -0.0304408159764
|
||||
102 101.0 -5.01779940929 -0.0295241620384
|
||||
103 102.0 -4.98876245596 -0.0285384716647
|
||||
104 103.0 -4.96074452928 -0.0274865961525
|
||||
105 104.0 -4.93381032851 -0.0263715306507
|
||||
106 105.0 -4.90802148862 -0.0251964075427
|
||||
107 106.0 -4.88343644644 -0.0239644895038
|
||||
108 107.0 -4.86011031397 -0.0226791622487
|
||||
109 108.0 -4.83809475914 -0.0213439269874
|
||||
110 109.0 -4.81743789414 -0.0199623926068
|
||||
111 110.0 -4.79818417182 -0.0185382675969
|
||||
112 111.0 -4.78037429015 -0.0170753517415
|
||||
113 112.0 -4.76404510526 -0.0155775275918
|
||||
114 113.0 -4.74922955293 -0.0140487517461
|
||||
115 114.0 -4.73595657904 -0.0124930459538
|
||||
116 115.0 -4.7242510789 -0.0109144880672
|
||||
117 116.0 -4.71413384576 -0.00931720286182
|
||||
118 117.0 -4.70562152846 -0.00770535274772
|
||||
119 118.0 -4.69872659855 -0.00608312839491
|
||||
120 119.0 -4.69345732669 -0.00445473929448
|
||||
121 120.0 -4.6898177686 -0.00282440427898
|
||||
122 121.0 -4.68780776044 -0.00119634202478
|
||||
123 122.0 -4.68742292374 0.000425238440527
|
||||
124 123.0 -4.68865467977 0.0020361472029
|
||||
125 124.0 -4.69149027336 0.00363222287571
|
||||
126 125.0 -4.69591280613 0.00520934194008
|
||||
127 126.0 -4.70190127895 0.0067634279891
|
||||
128 127.0 -4.70943064365 0.00829046085365
|
||||
129 128.0 -4.71847186379 0.00978648558781
|
||||
130 129.0 -4.72899198423 0.0112476212922
|
||||
131 130.0 -4.74095420961 0.0126700697544
|
||||
132 131.0 -4.7543179912 0.0140501238848
|
||||
133 132.0 -4.76903912216 0.0153841759291
|
||||
134 133.0 -4.78506984093 0.0166687254364
|
||||
135 134.0 -4.80235894235 0.0179003869651
|
||||
136 135.0 -4.82085189642 0.0190758975074
|
||||
137 136.0 -4.84049097437 0.0201921236154
|
||||
138 137.0 -4.86121538156 0.0212460682116
|
||||
139 138.0 -4.88296139722 0.0222348770682
|
||||
140 139.0 -4.90566252032 0.0231558449399
|
||||
141 140.0 -4.9292496215 0.0240064213355
|
||||
142 141.0 -4.95365110055 0.0247842159162
|
||||
143 142.0 -4.97879304911 0.0254870035063
|
||||
144 143.0 -5.00459941816 0.0261127287073
|
||||
145 144.0 -5.03099218995 0.0266595101027
|
||||
146 145.0 -5.05789155387 0.0271256440463
|
||||
147 146.0 -5.08521608601 0.0275096080241
|
||||
148 147.0 -5.11288293171 0.0278100635833
|
||||
149 148.0 -5.14080799097 0.0280258588231
|
||||
150 149.0 -5.16890610603 0.0281560304409
|
||||
151 150.0 -5.19709125082 0.0281998053314
|
||||
152 151.0 -5.22527672173 0.0281566017347
|
||||
153 152.0 -5.25337532941 0.0280260299338
|
||||
154 153.0 -5.28129959092 0.0278078924984
|
||||
155 154.0 -5.30896192196 0.0275021840788
|
||||
156 155.0 -5.33627482866 0.0271090907491
|
||||
157 156.0 -5.36315109852 0.0266289889046
|
||||
158 157.0 -5.38950398994 0.026062443717
|
||||
159 158.0 -5.41524742011 0.0254102071518
|
||||
160 159.0 -5.44029615055 0.0246732155563
|
||||
161 160.0 -5.46456597019 0.0238525868232
|
||||
162 161.0 -5.48797387528 0.0229496171403
|
||||
163 162.0 -5.51043824587 0.0219657773349
|
||||
164 163.0 -5.53187901853 0.0209027088232
|
||||
165 164.0 -5.55221785468 0.0197622191769
|
||||
166 165.0 -5.57137830441 0.0185462773191
|
||||
167 166.0 -5.58928596528 0.0172570083629
|
||||
168 167.0 -5.60586863576 0.0158966881068
|
||||
169 168.0 -5.62105646307 0.0144677372016
|
||||
170 169.0 -5.63478208493 0.0129727150063
|
||||
171 170.0 -5.64698076513 0.0114143131467
|
||||
172 171.0 -5.65759052241 0.00979534879707
|
||||
173 172.0 -5.66655225257 0.00811875770075
|
||||
174 173.0 -5.67380984344 0.00638758694863
|
||||
175 174.0 -5.67931028251 0.00460498753534
|
||||
176 175.0 -5.68300375706 0.00277420671195
|
||||
177 176.0 -5.68484374646 0.000898580155594
|
||||
178 177.0 -5.68478710669 -0.00101847602368
|
||||
179 178.0 -5.68279414663 -0.00297347341791
|
||||
180 179.0 -5.67882869631 -0.00496285957718
|
||||
181 180.0 -5.67285816674 -0.00698302636509
|
||||
182 181.0 -5.6648536014 -0.00903031839234
|
||||
183 182.0 -5.65478971926 -0.0111010415069
|
||||
184 183.0 -5.64264494925 -0.0131914713189
|
||||
185 184.0 -5.62840145627 -0.0152978617389
|
||||
186 185.0 -5.6120451586 -0.017416453508
|
||||
187 186.0 -5.59356573683 -0.0195434826976
|
||||
188 187.0 -5.57295663425 -0.0216751891584
|
||||
189 188.0 -5.55021504898 -0.0238078248974
|
||||
190 189.0 -5.52534191754 -0.0259376623617
|
||||
191 190.0 -5.4983418904 -0.0280610026087
|
||||
192 191.0 -5.46922329932 -0.0301741833429
|
||||
193 192.0 -5.43799811672 -0.0322735868002
|
||||
194 193.0 -5.40468190731 -0.0343556474589
|
||||
195 194.0 -5.36929377207 -0.0364168595607
|
||||
196 195.0 -5.33185628476 -0.0384537844225
|
||||
197 196.0 -5.29239542138 -0.0404630575223
|
||||
198 197.0 -5.25094048245 -0.0424413953416
|
||||
199 198.0 -5.20752400881 -0.0443856019501
|
||||
200 199.0 -5.16218169074 -0.0462925753151
|
||||
201 200.0 -5.11495227114 -0.0481593133234
|
||||
202 201.0 -5.06587744261 -0.0499829195012
|
||||
203 202.0 -5.01500173918 -0.0517606084187
|
||||
204 203.0 -4.96237242264 -0.0534897107689
|
||||
205 204.0 -4.90803936404 -0.055167678109
|
||||
206 205.0 -4.85205492059 -0.0567920872546
|
||||
207 206.0 -4.79447380837 -0.0583606443179
|
||||
208 207.0 -4.73535297113 -0.0598711883816
|
||||
209 208.0 -4.6747514457 -0.0613216948024
|
||||
210 209.0 -4.61273022413 -0.0627102781377
|
||||
211 210.0 -4.54935211328 -0.0640351946902
|
||||
212 211.0 -4.4846815919 -0.0652948446678
|
||||
213 212.0 -4.41878466581 -0.0664877739558
|
||||
214 213.0 -4.35172872155 -0.0676126754981
|
||||
215 214.0 -4.28358237872 -0.0686683902899
|
||||
216 215.0 -4.21441534165 -0.0696539079796
|
||||
217 216.0 -4.14429825061 -0.070568367083
|
||||
218 217.0 -4.07330253293 -0.0714110548116
|
||||
219 218.0 -4.00150025463 -0.0721814065199
|
||||
220 219.0 -3.92896397266 -0.072879004774
|
||||
221 220.0 -3.85576658834 -0.0735035780505
|
||||
222 221.0 -3.78198120223 -0.0740549990687
|
||||
223 222.0 -3.70768097086 -0.0745332827669
|
||||
224 223.0 -3.63293896573 -0.0749385839297
|
||||
225 224.0 -3.5578280347 -0.0752711944755
|
||||
226 225.0 -3.48242066643 -0.075531540416
|
||||
227 226.0 -3.4067888579 -0.0757201784978
|
||||
228 227.0 -3.33100398548 -0.0758377925383
|
||||
229 228.0 -3.25513667985 -0.0758851894693
|
||||
230 229.0 -3.17925670492 -0.0758632951011
|
||||
231 230.0 -3.10343284123 -0.0757731496217
|
||||
232 231.0 -3.02773277394 -0.0756159028468
|
||||
233 232.0 -2.95222298559 -0.0753928092342
|
||||
234 233.0 -2.87696865416 -0.0751052226812
|
||||
235 234.0 -2.80203355622 -0.0747545911191
|
||||
236 235.0 -2.72747997572 -0.0743424509249
|
||||
237 236.0 -2.65336861841 -0.073870421164
|
||||
238 237.0 -2.57975853208 -0.0733401976859
|
||||
239 238.0 -2.50670703279 -0.0727535470871
|
||||
240 239.0 -2.4342696372 -0.0721123005638
|
||||
241 240.0 -2.36250000104 -0.0714183476691
|
||||
242 241.0 -2.29144986396 -0.0706736299971
|
||||
243 242.0 -2.22116900065 -0.0698801348102
|
||||
244 243.0 -2.15170517837 -0.0690398886302
|
||||
245 244.0 -2.0831041209 -0.0681549508121
|
||||
246 245.0 -2.01540947892 -0.067227407119
|
||||
247 246.0 -1.94866280684 -0.0662593633171
|
||||
248 247.0 -1.88290354594 -0.0652529388105
|
||||
249 248.0 -1.81816901389 -0.0642102603325
|
||||
250 249.0 -1.7544944006 -0.0631334557138
|
||||
251 250.0 -1.69191277013 -0.0620246477436
|
||||
252 251.0 -1.6304550688 -0.0608859481423
|
||||
253 252.0 -1.57015013921 -0.059719451663
|
||||
254 253.0 -1.51102474011 -0.0585272303374
|
||||
255 254.0 -1.45310357187 -0.0573113278834
|
||||
256 255.0 -1.39640930762 -0.0560737542899
|
||||
257 256.0 -1.34096262951 -0.054816480593
|
||||
258 257.0 -1.28678227024 -0.0535414338587
|
||||
259 258.0 -1.23388505944 -0.0522504923856
|
||||
260 259.0 -1.18228597475 -0.0509454811405
|
||||
261 260.0 -1.13199819729 -0.0496281674395
|
||||
262 261.0 -1.08303317143 -0.0483002568854
|
||||
263 262.0 -1.03540066834 -0.046963389572
|
||||
264 263.0 -0.989108853377 -0.0456191365664
|
||||
265 264.0 -0.944164356669 -0.0442689966762
|
||||
266 265.0 -0.900572346917 -0.0429143935113
|
||||
267 266.0 -0.858336607922 -0.0415566728462
|
||||
268 267.0 -0.817459617608 -0.0401971002897
|
||||
269 268.0 -0.777942629232 -0.0388368592669
|
||||
270 269.0 -0.739785754436 -0.0374770493178
|
||||
271 270.0 -0.702988047855 -0.0361186847156
|
||||
272 271.0 -0.667547592939 -0.0347626934072
|
||||
273 272.0 -0.633461588675 -0.0334099162773
|
||||
274 273.0 -0.600726436882 -0.0320611067354
|
||||
275 274.0 -0.569337829756 -0.0307169306269
|
||||
276 275.0 -0.539290837348 -0.0293779664649
|
||||
277 276.0 -0.510579994645 -0.0280447059807
|
||||
278 277.0 -0.483199387947 -0.0267175549897
|
||||
279 278.0 -0.457142740217 -0.0253968345674
|
||||
280 279.0 -0.432403495111 -0.0240827825309
|
||||
281 280.0 -0.408974899365 -0.0227755552188
|
||||
282 281.0 -0.386850083265 -0.0214752295619
|
||||
283 282.0 -0.366022138902 -0.020181805438
|
||||
284 283.0 -0.346484195932 -0.0188952082997
|
||||
285 284.0 -0.328229494574 -0.0176152920667
|
||||
286 285.0 -0.311251455597 -0.0163418422722
|
||||
287 286.0 -0.295543747024 -0.0150745794496
|
||||
288 287.0 -0.28110034735 -0.0138131627512
|
||||
289 288.0 -0.267915605017 -0.0125571937823
|
||||
290 289.0 -0.255984293962 -0.011306220639
|
||||
291 290.0 -0.245301665026 -0.0100597421363
|
||||
292 291.0 -0.235863493049 -0.00881721220956
|
||||
293 292.0 -0.22766611948 -0.00757804447631
|
||||
294 293.0 -0.220706490355 -0.00634161694135
|
||||
295 294.0 -0.214982189503 -0.00510727682957
|
||||
296 295.0 -0.210491466861 -0.00387434552992
|
||||
297 296.0 -0.207233261801 -0.00264212363344
|
||||
298 297.0 -0.205207221373 -0.00140989604849
|
||||
299 298.0 -0.204413713408 -0.00017693717569
|
||||
300 299.0 -0.204853834414 0.0010574838751
|
||||
301 300.0 -0.206529412255 0.00229409804323
|
||||
302 301.0 -0.209443003569 0.00353363106913
|
||||
303 302.0 -0.213597885954 0.00477679825726
|
||||
304 303.0 -0.218998044922 0.00602429926791
|
||||
305 304.0 -0.22564815567 0.00727681295572
|
||||
306 305.0 -0.23355355972 0.00853499227222
|
||||
307 306.0 -0.2427202365 0.00979945924997
|
||||
308 307.0 -0.253154769958 0.0110708000854
|
||||
309 308.0 -0.264864310313 0.0123495603372
|
||||
310 309.0 -0.277856531075 0.0136362402565
|
||||
311 310.0 -0.292139581459 0.0149312902659
|
||||
312 311.0 -0.307722034364 0.0162351066015
|
||||
313 312.0 -0.324612830087 0.0175480271349
|
||||
314 313.0 -0.342821215943 0.0188703273888
|
||||
315 314.0 -0.362356682012 0.0202022167596
|
||||
316 315.0 -0.383228893218 0.0215438349636
|
||||
317 316.0 -0.405447617967 0.0228952487148
|
||||
318 317.0 -0.429022653586 0.0242564486517
|
||||
319 318.0 -0.45396374882 0.0256273465206
|
||||
320 319.0 -0.480280523637 0.0270077726275
|
||||
321 320.0 -0.507982386639 0.0283974735696
|
||||
322 321.0 -0.537078450328 0.029796110253
|
||||
323 322.0 -0.567577444555 0.0312032562068
|
||||
324 323.0 -0.59948762842 0.0326183962009
|
||||
325 324.0 -0.632816700956 0.0340409251716
|
||||
326 325.0 -0.667571710883 0.0354701474639
|
||||
327 326.0 -0.703758965776 0.0369052763923
|
||||
328 327.0 -0.741383940946 0.038345434125
|
||||
329 328.0 -0.780451188376 0.0397896518935
|
||||
330 329.0 -0.820964246018 0.0412368705304
|
||||
331 330.0 -0.862925547807 0.042685941334
|
||||
332 331.0 -0.906336334692 0.0441356272615
|
||||
333 332.0 -0.951196567028 0.045584604448
|
||||
334 333.0 -0.997504838648 0.0470314640498
|
||||
335 334.0 -1.04525829294 0.048474714408
|
||||
336 335.0 -1.09445254125 0.0499127835288
|
||||
337 336.0 -1.1450815839 0.0513440218749
|
||||
338 337.0 -1.1971377342 0.0527667054614
|
||||
339 338.0 -1.25061154564 0.0541790392498
|
||||
340 339.0 -1.30549174267 0.0555791608316
|
||||
341 340.0 -1.36176515529 0.0569651443923
|
||||
342 341.0 -1.41941665773 0.0583350049463
|
||||
343 342.0 -1.47842911151 0.0596867028317
|
||||
344 343.0 -1.53878331313 0.061018148454
|
||||
345 344.0 -1.60045794659 0.0623272072653
|
||||
346 345.0 -1.66342954101 0.0636117049668
|
||||
347 346.0 -1.72767243359 0.0648694329207
|
||||
348 347.0 -1.79315873807 0.0660981537565
|
||||
349 348.0 -1.85985831882 0.0672956071568
|
||||
350 349.0 -1.92773877092 0.0684595158069
|
||||
351 350.0 -1.99676540616 0.0695875914917
|
||||
352 351.0 -2.06690124527 0.0706775413231
|
||||
353 352.0 -2.13810701636 0.0717270740805
|
||||
354 353.0 -2.21034115987 0.0727339066469
|
||||
355 354.0 -2.28355983986 0.0736957705223
|
||||
356 355.0 -2.35771696194 0.0746104183955
|
||||
357 356.0 -2.43276419776 0.0754756307561
|
||||
358 357.0 -2.50865101613 0.0762892225281
|
||||
359 358.0 -2.58532472075 0.0770490497051
|
||||
360 359.0 -2.66273049463 0.0777530159679
|
||||
|
||||
# Table of the potential and its negative derivative for frustrated beta sheet
|
||||
# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
|
||||
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
|
||||
|
||||
FRUSTRATED_BETA
|
||||
N 360 DEGREES
|
||||
|
||||
1 0.0 -2.55809068762 0.0731724739818
|
||||
2 1.0 -2.63154144494 0.0737195744566
|
||||
3 2.0 -2.70551060968 0.0742089966437
|
||||
4 3.0 -2.77993963883 0.074639023134
|
||||
5 4.0 -2.85476830901 0.0750080115297
|
||||
6 5.0 -2.92993479441 0.0753144003899
|
||||
7 6.0 -3.00537575069 0.0755567150326
|
||||
8 7.0 -3.08102640456 0.0757335731758
|
||||
9 8.0 -3.15682064892 0.0758436903983
|
||||
10 9.0 -3.23269114341 0.075885885404
|
||||
11 10.0 -3.30856942003 0.0758590850738
|
||||
12 11.0 -3.38438599377 0.0757623292865
|
||||
13 12.0 -3.46007047791 0.0755947754951
|
||||
14 13.0 -3.53555170381 0.0753557030426
|
||||
15 14.0 -3.61075784476 0.0750445172025
|
||||
16 15.0 -3.68561654392 0.0746607529305
|
||||
17 16.0 -3.76005504566 0.0742040783151
|
||||
18 17.0 -3.83400033034 0.0736742977129
|
||||
19 18.0 -3.907379252 0.0730713545594
|
||||
20 19.0 -3.98011867868 0.0723953338429
|
||||
21 20.0 -4.0521456351 0.0716464642332
|
||||
22 21.0 -4.12338744726 0.0708251198546
|
||||
23 22.0 -4.19377188857 0.0699318216967
|
||||
24 23.0 -4.26322732737 0.0689672386556
|
||||
25 24.0 -4.33168287509 0.0679321881993
|
||||
26 25.0 -4.39906853508 0.0668276366524
|
||||
27 26.0 -4.46531535141 0.0656546990963
|
||||
28 27.0 -4.53035555742 0.0644146388823
|
||||
29 28.0 -4.59412272358 0.0631088667546
|
||||
30 29.0 -4.65655190431 0.061738939584
|
||||
31 30.0 -4.71757978327 0.0603065587109
|
||||
32 31.0 -4.77714481686 0.0588135679005
|
||||
33 32.0 -4.83518737548 0.057261950911
|
||||
34 33.0 -4.89164988211 0.0556538286799
|
||||
35 34.0 -4.94647694795 0.0539914561312
|
||||
36 35.0 -4.99961550465 0.0522772186102
|
||||
37 36.0 -5.05101493277 0.0505136279528
|
||||
38 37.0 -5.10062718621 0.048703318195
|
||||
39 38.0 -5.14840691207 0.0468490409338
|
||||
40 39.0 -5.19431156578 0.0449536603471
|
||||
41 40.0 -5.23830152101 0.0430201478838
|
||||
42 41.0 -5.28034017422 0.0410515766363
|
||||
43 42.0 -5.3203940433 0.0390511154063
|
||||
44 43.0 -5.35843286021 0.0370220224793
|
||||
45 44.0 -5.39442965726 0.0349676391193
|
||||
46 45.0 -5.4283608467 0.0328913828015
|
||||
47 46.0 -5.46020629342 0.0307967401964
|
||||
48 47.0 -5.48994938059 0.028687259923
|
||||
49 48.0 -5.51757706789 0.0265665450883
|
||||
50 49.0 -5.54307994213 0.0244382456298
|
||||
51 50.0 -5.56645226024 0.0223060504811
|
||||
52 51.0 -5.58769198425 0.0201736795783
|
||||
53 52.0 -5.60680080825 0.0180448757265
|
||||
54 53.0 -5.62378417713 0.0159233963481
|
||||
55 54.0 -5.63865129702 0.0138130051308
|
||||
56 55.0 -5.6514151374 0.0117174635982
|
||||
57 56.0 -5.66209242462 0.00964052262251
|
||||
58 57.0 -5.67070362704 0.00758591390103
|
||||
59 58.0 -5.67727293157 0.00555734141841
|
||||
60 59.0 -5.6818282117 0.00355847291538
|
||||
61 60.0 -5.68440098698 0.00159293138608
|
||||
62 61.0 -5.68502637408 -0.000335713374531
|
||||
63 62.0 -5.68374302934 -0.00222395315148
|
||||
64 63.0 -5.68059308309 -0.0040683495974
|
||||
65 64.0 -5.67562206565 -0.00586554240548
|
||||
66 65.0 -5.66887882528 -0.00761225734683
|
||||
67 66.0 -5.66041543813 -0.00930531415106
|
||||
68 67.0 -5.65028711044 -0.0109416342099
|
||||
69 68.0 -5.63855207307 -0.0125182480831
|
||||
70 69.0 -5.6252714687 -0.0140323027883
|
||||
71 70.0 -5.61050923182 -0.0154810688529
|
||||
72 71.0 -5.59433196178 -0.0168619471125
|
||||
73 72.0 -5.57680878923 -0.0181724752358
|
||||
74 73.0 -5.5580112361 -0.019410333958
|
||||
75 74.0 -5.53801306959 -0.0205733530082
|
||||
76 75.0 -5.51689015031 -0.0216595167121
|
||||
77 76.0 -5.49472027505 -0.0226669692568
|
||||
78 77.0 -5.47158301441 -0.0235940196022
|
||||
79 78.0 -5.44755954575 -0.0244391460249
|
||||
80 79.0 -5.42273248172 -0.0252010002837
|
||||
81 80.0 -5.3971856949 -0.0258784113929
|
||||
82 81.0 -5.37100413881 -0.0264703889936
|
||||
83 82.0 -5.34427366574 -0.0269761263135
|
||||
84 83.0 -5.31708084192 -0.0273950027051
|
||||
85 84.0 -5.28951276022 -0.0277265857564
|
||||
86 85.0 -5.26165685114 -0.0279706329651
|
||||
87 86.0 -5.23360069216 -0.0281270929735
|
||||
88 87.0 -5.20543181621 -0.0281961063563
|
||||
89 88.0 -5.17723751951 -0.0281780059613
|
||||
90 89.0 -5.14910466934 -0.0280733167983
|
||||
91 90.0 -5.12111951208 -0.0278827554757
|
||||
92 91.0 -5.09336748214 -0.0276072291861
|
||||
93 92.0 -5.06593301201 -0.0272478342399
|
||||
94 93.0 -5.0388993441 -0.026805854151
|
||||
95 94.0 -5.01234834466 -0.0262827572773
|
||||
96 95.0 -4.98636032033 -0.0256801940208
|
||||
97 96.0 -4.96101383762 -0.0249999935924
|
||||
98 97.0 -4.93638554598 -0.0242441603499
|
||||
99 98.0 -4.91255000457 -0.0234148697145
|
||||
100 99.0 -4.88957951348 -0.0225144636776
|
||||
101 100.0 -4.86754394953 -0.0215454459053
|
||||
102 101.0 -4.84651060724 -0.0205104764546
|
||||
103 102.0 -4.8265440452 -0.01941236611
|
||||
104 103.0 -4.80770593836 -0.0182540703564
|
||||
105 104.0 -4.79005493648 -0.0170386830008
|
||||
106 105.0 -4.77364652914 -0.0157694294583
|
||||
107 106.0 -4.7585329176 -0.0144496597171
|
||||
108 107.0 -4.74476289391 -0.0130828410011
|
||||
109 108.0 -4.73238172744 -0.0116725501446
|
||||
110 109.0 -4.72143105919 -0.0102224657007
|
||||
111 110.0 -4.71194880414 -0.00873635979846
|
||||
112 111.0 -4.70396906182 -0.0072180897712
|
||||
113 112.0 -4.69752203541 -0.00567158957449
|
||||
114 113.0 -4.69263395945 -0.00410086101469
|
||||
115 114.0 -4.68932703648 -0.00250996480925
|
||||
116 115.0 -4.68761938265 -0.000903011500147
|
||||
117 116.0 -4.68752498248 0.00071584775762
|
||||
118 117.0 -4.68905365291 0.00234243051027
|
||||
119 118.0 -4.69221101668 0.00397253239976
|
||||
120 119.0 -4.69699848518 0.00560193661579
|
||||
121 120.0 -4.70341325069 0.00722642338265
|
||||
122 121.0 -4.71144828821 0.00884177945771
|
||||
123 122.0 -4.72109236669 0.0104438076188
|
||||
124 123.0 -4.73233006984 0.0120283361174
|
||||
125 124.0 -4.74514182625 0.0135912280748
|
||||
126 125.0 -4.75950394898 0.0151283907985
|
||||
127 126.0 -4.77538868431 0.0166357849963
|
||||
128 127.0 -4.79276426974 0.0181094338658
|
||||
129 128.0 -4.81159500092 0.0195454320375
|
||||
130 129.0 -4.83184130754 0.0209399543498
|
||||
131 130.0 -4.8534598378 0.0222892644342
|
||||
132 131.0 -4.87640355143 0.0235897230915
|
||||
133 132.0 -4.90062182095 0.0248377964369
|
||||
134 133.0 -4.92606054096 0.0260300637961
|
||||
135 134.0 -4.95266224518 0.0271632253326
|
||||
136 135.0 -4.98036623096 0.028234109388
|
||||
137 136.0 -5.00910869107 0.0292396795182
|
||||
138 137.0 -5.03882285221 0.0301770412082
|
||||
139 138.0 -5.06943912022 0.0310434482505
|
||||
140 139.0 -5.10088523142 0.0318363087705
|
||||
141 140.0 -5.13308640979 0.0325531908865
|
||||
142 141.0 -5.16596552963 0.0331918279898
|
||||
143 142.0 -5.19944328334 0.0337501236332
|
||||
144 143.0 -5.23343835383 0.0342261560164
|
||||
145 144.0 -5.26786759123 0.0346181820585
|
||||
146 145.0 -5.30264619353 0.0349246410472
|
||||
147 146.0 -5.33768789051 0.0351441578585
|
||||
148 147.0 -5.37290513082 0.0352755457383
|
||||
149 148.0 -5.40820927152 0.0353178086401
|
||||
150 149.0 -5.4435107698 0.0352701431151
|
||||
151 150.0 -5.4787193763 0.0351319397498
|
||||
152 151.0 -5.51374432971 0.0349027841491
|
||||
153 152.0 -5.54849455206 0.0345824574643
|
||||
154 153.0 -5.58287884436 0.0341709364636
|
||||
155 154.0 -5.61680608206 0.0336683931487
|
||||
156 155.0 -5.65018540988 0.0330751939177
|
||||
157 156.0 -5.68292643563 0.0323918982779
|
||||
158 157.0 -5.71493942249 0.0316192571138
|
||||
159 158.0 -5.74613547931 0.0307582105139
|
||||
160 159.0 -5.77642674856 0.029809885165
|
||||
161 160.0 -5.80572659147 0.0287755913197
|
||||
162 161.0 -5.83394976986 0.0276568193473
|
||||
163 162.0 -5.86101262442 0.0264552358763
|
||||
164 163.0 -5.8868332488 0.025172679541
|
||||
165 164.0 -5.91133165941 0.0238111563427
|
||||
166 165.0 -5.93442996024 0.0223728346376
|
||||
167 166.0 -5.95605250261 0.0208600397671
|
||||
168 167.0 -5.97612603931 0.0192752483425
|
||||
169 168.0 -5.99457987285 0.0176210822011
|
||||
170 169.0 -6.01134599757 0.015900302049
|
||||
171 170.0 -6.02635923519 0.014115800807
|
||||
172 171.0 -6.03955736358 0.0122705966784
|
||||
173 172.0 -6.05088123845 0.0103678259555
|
||||
174 173.0 -6.0602749078 0.00841073558436
|
||||
175 174.0 -6.06768571866 0.00640267550713
|
||||
176 175.0 -6.0730644163 0.00434709080102
|
||||
177 176.0 -6.07636523524 0.00224751363529
|
||||
178 177.0 -6.07754598232 0.000107555066143
|
||||
179 178.0 -6.07656811141 -0.00206910330914
|
||||
180 179.0 -6.07339678973 -0.00427871781763
|
||||
181 180.0 -6.06800095563 -0.00651749127408
|
||||
182 181.0 -6.06035336781 -0.00878158162059
|
||||
183 182.0 -6.05043064586 -0.0110671106207
|
||||
184 183.0 -6.03821330204 -0.0133701725859
|
||||
185 184.0 -6.02368576439 -0.0156868431131
|
||||
186 185.0 -6.00683639108 -0.0180131878107
|
||||
187 186.0 -5.98765747603 -0.0203452709919
|
||||
188 187.0 -5.96614524589 -0.0226791643135
|
||||
189 188.0 -5.94229984843 -0.025010955339
|
||||
190 189.0 -5.91612533236 -0.0273367560054
|
||||
191 190.0 -5.88762961878 -0.0296527109716
|
||||
192 191.0 -5.85682446433 -0.0319550058299
|
||||
193 192.0 -5.82372541626 -0.0342398751598
|
||||
194 193.0 -5.78835175943 -0.0365036104045
|
||||
195 194.0 -5.75072645562 -0.0387425675516
|
||||
196 195.0 -5.71087607524 -0.0409531746008
|
||||
197 196.0 -5.66883072166 -0.0431319387984
|
||||
198 197.0 -5.62462394846 -0.0452754536249
|
||||
199 198.0 -5.57829266983 -0.0473804055171
|
||||
200 199.0 -5.5298770643 -0.0494435803104
|
||||
201 200.0 -5.47942047235 -0.0514618693867
|
||||
202 201.0 -5.42696928781 -0.0534322755136
|
||||
203 202.0 -5.37257284377 -0.055351918363
|
||||
204 203.0 -5.316283293 -0.0572180396955
|
||||
205 204.0 -5.25815548345 -0.059028008202
|
||||
206 205.0 -5.19824682901 -0.0607793239895
|
||||
207 206.0 -5.13661717604 -0.0624696227052
|
||||
208 207.0 -5.0733286659 -0.0640966792879
|
||||
209 208.0 -5.00844559393 -0.0656584113417
|
||||
210 209.0 -4.94203426529 -0.0671528821253
|
||||
211 210.0 -4.87416284794 -0.0685783031513
|
||||
212 211.0 -4.80490122327 -0.0699330363936
|
||||
213 212.0 -4.7343208347 -0.0712155960973
|
||||
214 213.0 -4.66249453466 -0.0724246501921
|
||||
215 214.0 -4.58949643037 -0.0735590213066
|
||||
216 215.0 -4.51540172879 -0.0746176873849
|
||||
217 216.0 -4.44028658118 -0.0755997819067
|
||||
218 217.0 -4.3642279276 -0.0765045937139
|
||||
219 218.0 -4.28730334182 -0.0773315664459
|
||||
220 219.0 -4.20959087694 -0.0780802975905
|
||||
221 220.0 -4.13116891218 -0.0787505371538
|
||||
222 221.0 -4.0521160012 -0.0793421859574
|
||||
223 222.0 -3.97251072229 -0.0798552935693
|
||||
224 223.0 -3.89243153076 -0.0802900558785
|
||||
225 224.0 -3.81195661404 -0.0806468123209
|
||||
226 225.0 -3.73116374964 -0.0809260427693
|
||||
227 226.0 -3.65013016636 -0.0811283640964
|
||||
228 227.0 -3.56893240921 -0.0812545264246
|
||||
229 228.0 -3.48764620813 -0.0813054090744
|
||||
230 229.0 -3.4063463509 -0.0812820162266
|
||||
231 230.0 -3.32510656064 -0.0811854723104
|
||||
232 231.0 -3.24399937793 -0.081017017134
|
||||
233 232.0 -3.16309604794 -0.0807780007742
|
||||
234 233.0 -3.08246641287 -0.0804698782381
|
||||
235 234.0 -3.00217880976 -0.0800942039176
|
||||
236 235.0 -2.92229997393 -0.079652625851
|
||||
237 236.0 -2.84289494829 -0.0791468798106
|
||||
238 237.0 -2.76402699866 -0.0785787832348
|
||||
239 238.0 -2.68575753514 -0.0779502290223
|
||||
240 239.0 -2.60814603984 -0.077263179207
|
||||
241 240.0 -2.53125000097 -0.0765196585342
|
||||
242 241.0 -2.4551248533 -0.0757217479546
|
||||
243 242.0 -2.37982392531 -0.0748715780578
|
||||
244 243.0 -2.30539839282 -0.073971322463
|
||||
245 244.0 -2.23189723927 -0.0730231911866
|
||||
246 245.0 -2.15936722267 -0.072029424007
|
||||
247 246.0 -2.0878528491 -0.0709922838436
|
||||
248 247.0 -2.01739635293 -0.0699140501714
|
||||
249 248.0 -1.94803768347 -0.0687970124882
|
||||
250 249.0 -1.87981449824 -0.0676434638537
|
||||
251 250.0 -1.81276216256 -0.0664556945194
|
||||
252 251.0 -1.74691375554 -0.0652359856651
|
||||
253 252.0 -1.68230008218 -0.0639866032624
|
||||
254 253.0 -1.61894969164 -0.0627097920793
|
||||
255 254.0 -1.55688890134 -0.0614077698443
|
||||
256 255.0 -1.49614182687 -0.0600827215855
|
||||
257 256.0 -1.43673041741 -0.05873679416
|
||||
258 257.0 -1.37867449659 -0.0573720909874
|
||||
259 258.0 -1.32199180845 -0.0559906670036
|
||||
260 259.0 -1.26669806833 -0.0545945238457
|
||||
261 260.0 -1.21280701853 -0.0531856052829
|
||||
262 261.0 -1.1603304883 -0.0517657929031
|
||||
263 262.0 -1.1092784581 -0.0503369020679
|
||||
264 263.0 -1.05965912771 -0.0489006781451
|
||||
265 264.0 -1.01147898802 -0.0474587930279
|
||||
266 265.0 -0.964742896092 -0.0460128419505
|
||||
267 266.0 -0.919454153297 -0.0445643406057
|
||||
268 267.0 -0.875614586172 -0.0431147225719
|
||||
269 268.0 -0.833224629688 -0.0416653370554
|
||||
270 269.0 -0.792283412613 -0.0402174469521
|
||||
271 270.0 -0.752788844664 -0.038772227232
|
||||
272 271.0 -0.714737705101 -0.0373307636499
|
||||
273 272.0 -0.67812573245 -0.0358940517831
|
||||
274 273.0 -0.642947715028 -0.0344629963972
|
||||
275 274.0 -0.609197581934 -0.0330384111393
|
||||
276 275.0 -0.576868494182 -0.0316210185584
|
||||
277 276.0 -0.545952935658 -0.0302114504483
|
||||
278 277.0 -0.51644280357 -0.0288102485125
|
||||
279 278.0 -0.488329498068 -0.0274178653447
|
||||
280 279.0 -0.461604010741 -0.0260346657211
|
||||
281 280.0 -0.436257011655 -0.0246609281969
|
||||
282 281.0 -0.412278934657 -0.023296847002
|
||||
283 282.0 -0.389660060626 -0.0219425342253
|
||||
284 283.0 -0.368390598407 -0.0205980222818
|
||||
285 284.0 -0.348460763137 -0.01926326665
|
||||
286 285.0 -0.329860851704 -0.0179381488715
|
||||
287 286.0 -0.312581315078 -0.0166224797996
|
||||
288 287.0 -0.296612827279 -0.015316003087
|
||||
289 288.0 -0.281946350734 -0.0140183988977
|
||||
290 289.0 -0.268573197826 -0.0127292878319
|
||||
291 290.0 -0.256485088408 -0.0114482350481
|
||||
292 291.0 -0.245674203109 -0.0101747545698
|
||||
293 292.0 -0.236133232246 -0.00890831375923
|
||||
294 293.0 -0.227855420178 -0.00764833794542
|
||||
295 294.0 -0.220834604976 -0.00639421518813
|
||||
296 295.0 -0.215065253253 -0.00514530116277
|
||||
297 296.0 -0.210542490065 -0.00390092414876
|
||||
298 297.0 -0.207262123775 -0.00266039010467
|
||||
299 298.0 -0.205220665805 -0.00142298781263
|
||||
300 299.0 -0.204415345223 -0.000187994074493
|
||||
301 300.0 -0.204844118104 0.00104532105779
|
||||
302 301.0 -0.206505671662 0.00227768903543
|
||||
303 302.0 -0.209399423126 0.0035098375675
|
||||
304 303.0 -0.213525513386 0.00474248539479
|
||||
305 304.0 -0.218884795423 0.00597633710062
|
||||
306 305.0 -0.225478817581 0.00721207797616
|
||||
307 306.0 -0.233309801737 0.00845036895769
|
||||
308 307.0 -0.242380616448 0.00969184165314
|
||||
309 308.0 -0.252694745185 0.0109370934746
|
||||
310 309.0 -0.264256249747 0.0121866828936
|
||||
311 310.0 -0.277069729013 0.0134411248358
|
||||
312 311.0 -0.291140273151 0.0147008862297
|
||||
313 312.0 -0.306473413467 0.0159663817261
|
||||
314 313.0 -0.323075068066 0.0172379696031
|
||||
315 314.0 -0.340951483513 0.018515947869
|
||||
316 315.0 -0.360109172702 0.0198005505798
|
||||
317 316.0 -0.380554849155 0.0210919443819
|
||||
318 317.0 -0.402295357987 0.0223902252933
|
||||
319 318.0 -0.425337603767 0.0236954157356
|
||||
320 319.0 -0.449688475549 0.0250074618263
|
||||
321 320.0 -0.475354769327 0.0263262309427
|
||||
322 321.0 -0.50234310819 0.0276515095659
|
||||
323 322.0 -0.530659860472 0.0289830014145
|
||||
324 323.0 -0.560311056174 0.0303203258736
|
||||
325 324.0 -0.59130230198 0.0316630167284
|
||||
326 325.0 -0.623638695141 0.0330105212056
|
||||
327 326.0 -0.657324736579 0.0343621993296
|
||||
328 327.0 -0.692364243488 0.0357173235955
|
||||
329 328.0 -0.728760261774 0.0370750789637
|
||||
330 329.0 -0.766514978659 0.0384345631765
|
||||
331 330.0 -0.805629635748 0.0397947873984
|
||||
332 331.0 -0.846104442913 0.04115467718
|
||||
333 332.0 -0.887938493289 0.042513073745
|
||||
334 333.0 -0.93112967973 0.0438687355968
|
||||
335 334.0 -0.975674613021 0.0452203404434
|
||||
336 335.0 -1.02156854218 0.0465664874361
|
||||
337 336.0 -1.06880527714 0.0479056997168
|
||||
338 337.0 -1.11737711415 0.0492364272675
|
||||
339 338.0 -1.16727476416 0.0505570500574
|
||||
340 339.0 -1.2184872845 0.051865881477
|
||||
341 340.0 -1.27100201415 0.0531611720525
|
||||
342 341.0 -1.32480451282 0.0544411134304
|
||||
343 342.0 -1.37987850417 0.055703842622
|
||||
344 343.0 -1.43620582346 0.0569474464963
|
||||
345 344.0 -1.49376636966 0.0581699665097
|
||||
346 345.0 -1.55253806258 0.05936940366
|
||||
347 346.0 -1.61249680493 0.0605437236497
|
||||
348 347.0 -1.67361644969 0.0616908622471
|
||||
349 348.0 -1.73586877296 0.0628087308273
|
||||
350 349.0 -1.79922345238 0.0638952220804
|
||||
351 350.0 -1.86364805137 0.0649482158688
|
||||
352 351.0 -1.92910800931 0.0659655852184
|
||||
353 352.0 -1.9955666377 0.066945202426
|
||||
354 353.0 -2.06298512258 0.0678849452658
|
||||
355 354.0 -2.13132253309 0.0687827032771
|
||||
356 355.0 -2.20053583647 0.0696363841147
|
||||
357 356.0 -2.27057991931 0.0704439199439
|
||||
358 357.0 -2.3414076153 0.0712032738621
|
||||
359 358.0 -2.41296973939 0.0719124463259
|
||||
360 359.0 -2.48521512832 0.072569481568
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
@ -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 ../
|
||||
@ -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.)
|
||||
@ -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
|
||||
34 2 3 3 0.000000 1.0000 0
|
||||
35 2 3 3 0.000000 1.0000 0
|
||||
36 2 1 1 0.000000 1.0000 0
|
||||
37 2 2 2 0.000000 1.0000 0
|
||||
38 2 1 1 0.000000 1.0000 0
|
||||
39 2 2 2 0.000000 1.0000 0
|
||||
40 2 1 1 0.000000 1.0000 0
|
||||
41 2 2 2 0.000000 1.0000 0
|
||||
42 2 3 3 0.000000 1.0000 0
|
||||
43 2 3 3 0.000000 1.0000 0
|
||||
44 2 3 3 0.000000 1.0000 0
|
||||
45 2 1 1 0.000000 1.0000 0
|
||||
46 2 1 1 0.000000 1.0000 0
|
||||
47 2 2 2 0.000000 1.0000 0
|
||||
48 2 2 2 0.000000 1.0000 0
|
||||
49 2 1 1 0.000000 1.0000 0
|
||||
50 2 1 1 0.000000 1.0000 0
|
||||
51 2 2 2 0.000000 1.0000 0
|
||||
52 2 2 2 0.000000 1.0000 0
|
||||
53 2 1 1 0.000000 1.0000 0
|
||||
54 2 2 2 0.000000 1.0000 0
|
||||
55 3 2 2 0.000000 1.0000 0
|
||||
56 3 1 1 0.000000 1.0000 0
|
||||
57 3 2 2 0.000000 1.0000 0
|
||||
58 3 1 1 0.000000 1.0000 0
|
||||
59 3 2 2 0.000000 1.0000 0
|
||||
60 3 1 1 0.000000 1.0000 0
|
||||
61 3 3 3 0.000000 1.0000 0
|
||||
62 3 3 3 0.000000 1.0000 0
|
||||
63 3 1 1 0.000000 1.0000 0
|
||||
64 3 2 2 0.000000 1.0000 0
|
||||
65 3 1 1 0.000000 1.0000 0
|
||||
66 3 2 2 0.000000 1.0000 0
|
||||
67 3 1 1 0.000000 1.0000 0
|
||||
68 3 2 2 0.000000 1.0000 0
|
||||
69 3 3 3 0.000000 1.0000 0
|
||||
70 3 3 3 0.000000 1.0000 0
|
||||
71 3 3 3 0.000000 1.0000 0
|
||||
72 3 1 1 0.000000 1.0000 0
|
||||
73 3 1 1 0.000000 1.0000 0
|
||||
74 3 2 2 0.000000 1.0000 0
|
||||
75 3 2 2 0.000000 1.0000 0
|
||||
76 3 1 1 0.000000 1.0000 0
|
||||
77 3 1 1 0.000000 1.0000 0
|
||||
78 3 2 2 0.000000 1.0000 0
|
||||
79 3 2 2 0.000000 1.0000 0
|
||||
80 3 1 1 0.000000 1.0000 0
|
||||
81 3 2 2 0.000000 1.0000 0
|
||||
82 4 2 2 0.000000 1.0000 0
|
||||
83 4 1 1 0.000000 1.0000 0
|
||||
84 4 2 2 0.000000 1.0000 0
|
||||
85 4 1 1 0.000000 1.0000 0
|
||||
86 4 2 2 0.000000 1.0000 0
|
||||
87 4 1 1 0.000000 1.0000 0
|
||||
88 4 3 3 0.000000 1.0000 0
|
||||
89 4 3 3 0.000000 1.0000 0
|
||||
90 4 1 1 0.000000 1.0000 0
|
||||
91 4 2 2 0.000000 1.0000 0
|
||||
92 4 1 1 0.000000 1.0000 0
|
||||
93 4 2 2 0.000000 1.0000 0
|
||||
94 4 1 1 0.000000 1.0000 0
|
||||
95 4 2 2 0.000000 1.0000 0
|
||||
96 4 3 3 0.000000 1.0000 0
|
||||
97 4 3 3 0.000000 1.0000 0
|
||||
98 4 3 3 0.000000 1.0000 0
|
||||
99 4 1 1 0.000000 1.0000 0
|
||||
100 4 1 1 0.000000 1.0000 0
|
||||
101 4 2 2 0.000000 1.0000 0
|
||||
102 4 2 2 0.000000 1.0000 0
|
||||
103 4 1 1 0.000000 1.0000 0
|
||||
104 4 1 1 0.000000 1.0000 0
|
||||
105 4 2 2 0.000000 1.0000 0
|
||||
106 4 2 2 0.000000 1.0000 0
|
||||
107 4 1 1 0.000000 1.0000 0
|
||||
108 4 2 2 0.000000 1.0000 0
|
||||
109 5 2 2 0.000000 1.0000 0
|
||||
110 5 1 1 0.000000 1.0000 0
|
||||
111 5 2 2 0.000000 1.0000 0
|
||||
112 5 1 1 0.000000 1.0000 0
|
||||
113 5 2 2 0.000000 1.0000 0
|
||||
114 5 1 1 0.000000 1.0000 0
|
||||
115 5 3 3 0.000000 1.0000 0
|
||||
116 5 3 3 0.000000 1.0000 0
|
||||
117 5 1 1 0.000000 1.0000 0
|
||||
118 5 2 2 0.000000 1.0000 0
|
||||
119 5 1 1 0.000000 1.0000 0
|
||||
120 5 2 2 0.000000 1.0000 0
|
||||
121 5 1 1 0.000000 1.0000 0
|
||||
122 5 2 2 0.000000 1.0000 0
|
||||
123 5 3 3 0.000000 1.0000 0
|
||||
124 5 3 3 0.000000 1.0000 0
|
||||
125 5 3 3 0.000000 1.0000 0
|
||||
126 5 1 1 0.000000 1.0000 0
|
||||
127 5 1 1 0.000000 1.0000 0
|
||||
128 5 2 2 0.000000 1.0000 0
|
||||
129 5 2 2 0.000000 1.0000 0
|
||||
130 5 1 1 0.000000 1.0000 0
|
||||
131 5 1 1 0.000000 1.0000 0
|
||||
132 5 2 2 0.000000 1.0000 0
|
||||
133 5 2 2 0.000000 1.0000 0
|
||||
134 5 1 1 0.000000 1.0000 0
|
||||
135 5 2 2 0.000000 1.0000 0
|
||||
136 6 2 2 0.000000 1.0000 0
|
||||
137 6 1 1 0.000000 1.0000 0
|
||||
138 6 2 2 0.000000 1.0000 0
|
||||
139 6 1 1 0.000000 1.0000 0
|
||||
140 6 2 2 0.000000 1.0000 0
|
||||
141 6 1 1 0.000000 1.0000 0
|
||||
142 6 3 3 0.000000 1.0000 0
|
||||
143 6 3 3 0.000000 1.0000 0
|
||||
144 6 1 1 0.000000 1.0000 0
|
||||
145 6 2 2 0.000000 1.0000 0
|
||||
146 6 1 1 0.000000 1.0000 0
|
||||
147 6 2 2 0.000000 1.0000 0
|
||||
148 6 1 1 0.000000 1.0000 0
|
||||
149 6 2 2 0.000000 1.0000 0
|
||||
150 6 3 3 0.000000 1.0000 0
|
||||
151 6 3 3 0.000000 1.0000 0
|
||||
152 6 3 3 0.000000 1.0000 0
|
||||
153 6 1 1 0.000000 1.0000 0
|
||||
154 6 1 1 0.000000 1.0000 0
|
||||
155 6 2 2 0.000000 1.0000 0
|
||||
156 6 2 2 0.000000 1.0000 0
|
||||
157 6 1 1 0.000000 1.0000 0
|
||||
158 6 1 1 0.000000 1.0000 0
|
||||
159 6 2 2 0.000000 1.0000 0
|
||||
160 6 2 2 0.000000 1.0000 0
|
||||
161 6 1 1 0.000000 1.0000 0
|
||||
162 6 2 2 0.000000 1.0000 0
|
||||
163 7 2 2 0.000000 1.0000 0
|
||||
164 7 1 1 0.000000 1.0000 0
|
||||
165 7 2 2 0.000000 1.0000 0
|
||||
166 7 1 1 0.000000 1.0000 0
|
||||
167 7 2 2 0.000000 1.0000 0
|
||||
168 7 1 1 0.000000 1.0000 0
|
||||
169 7 3 3 0.000000 1.0000 0
|
||||
170 7 3 3 0.000000 1.0000 0
|
||||
171 7 1 1 0.000000 1.0000 0
|
||||
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
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 30 KiB |
Binary file not shown.
|
Before Width: | Height: | Size: 26 KiB |
@ -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
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -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))
|
||||
|
||||
@ -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))
|
||||
|
||||
@ -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.
|
||||
@ -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)
|
||||
}
|
||||
@ -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 -4.56769153408 0.0738800794563
|
||||
25 24.0 -4.64102186743 0.0727680008923
|
||||
26 25.0 -4.71320253365 0.0715809208518
|
||||
27 26.0 -4.78415908407 0.0703199708131
|
||||
28 27.0 -4.85381827903 0.0689864371778
|
||||
29 28.0 -4.92210824234 0.067581760373
|
||||
30 29.0 -4.98895861476 0.0661075335571
|
||||
31 30.0 -5.05430070586 0.0645655009259
|
||||
32 31.0 -5.11806764409 0.0629575556235
|
||||
33 32.0 -5.18019452449 0.061285737258
|
||||
34 33.0 -5.24061855376 0.0595522290273
|
||||
35 34.0 -5.29927919225 0.0577593544584
|
||||
36 35.0 -5.3561182925 0.0559095737673
|
||||
37 36.0 -5.41108023395 0.0540054798439
|
||||
38 37.0 -5.46411205346 0.0520497938726
|
||||
39 38.0 -5.51516357127 0.0500453605949
|
||||
40 39.0 -5.56418751203 0.0479951432253
|
||||
41 40.0 -5.61113962059 0.0459022180302
|
||||
42 41.0 -5.65597877221 0.0437697685824
|
||||
43 42.0 -5.69866707689 0.0416010797029
|
||||
44 43.0 -5.7391699774 0.0393995311046
|
||||
45 44.0 -5.77745634094 0.0371685907508
|
||||
46 45.0 -5.81349854393 0.034911807945
|
||||
47 46.0 -5.84727254977 0.0326328061676
|
||||
48 47.0 -5.87875797937 0.030335275675
|
||||
49 48.0 -5.90793817411 0.0280229658805
|
||||
50 49.0 -5.93480025113 0.0256996775336
|
||||
51 50.0 -5.95933515063 0.0233692547166
|
||||
52 51.0 -5.98153767519 0.0210355766777
|
||||
53 52.0 -6.00140652074 0.0187025495211
|
||||
54 53.0 -6.01894429926 0.016374097773
|
||||
55 54.0 -6.03415755288 0.0140541558448
|
||||
56 55.0 -6.04705675953 0.0117466594146
|
||||
57 56.0 -6.05765632981 0.00945553674764
|
||||
58 57.0 -6.06597459526 0.00718469997761
|
||||
59 58.0 -6.07203378786 0.00493803637051
|
||||
60 59.0 -6.07586001075 0.00271939959245
|
||||
61 60.0 -6.07748320034 0.000532601003776
|
||||
62 61.0 -6.07693707962 -0.00161859899905
|
||||
63 62.0 -6.07425910291 -0.00373049957158
|
||||
64 63.0 -6.06949039207 -0.00579946791801
|
||||
65 64.0 -6.06267566421 -0.00782194767468
|
||||
66 65.0 -6.05386315117 -0.00979446715893
|
||||
67 66.0 -6.04310451074 -0.0117136474624
|
||||
68 67.0 -6.03045472992 -0.0135762103679
|
||||
69 68.0 -6.01597202036 -0.0153789860691
|
||||
70 69.0 -5.99971770618 -0.0171189206741
|
||||
71 70.0 -5.98175610439 -0.0187930834719
|
||||
72 71.0 -5.9621543982 -0.0203986739443
|
||||
73 72.0 -5.9409825034 -0.0219330285036
|
||||
74 73.0 -5.91831292823 -0.0233936269399
|
||||
75 74.0 -5.89422062685 -0.0247780985587
|
||||
76 75.0 -5.86878284696 -0.0260842279959
|
||||
77 76.0 -5.84207897162 -0.0273099606906
|
||||
78 77.0 -5.81419035593 -0.0284534080045
|
||||
79 78.0 -5.78520015867 -0.0295128519729
|
||||
80 79.0 -5.7551931694 -0.0304867496727
|
||||
81 80.0 -5.72425563141 -0.0313737371989
|
||||
82 81.0 -5.6924750609 -0.0321726332348
|
||||
83 82.0 -5.65994006273 -0.0328824422092
|
||||
84 83.0 -5.62674014332 -0.0335023570292
|
||||
85 84.0 -5.59296552097 -0.0340317613814
|
||||
86 85.0 -5.55870693409 -0.0344702315961
|
||||
87 86.0 -5.52405544786 -0.0348175380654
|
||||
88 87.0 -5.48910225957 -0.0350736462148
|
||||
89 88.0 -5.45393850338 -0.0352387170203
|
||||
90 89.0 -5.41865505462 -0.0353131070729
|
||||
91 90.0 -5.38334233438 -0.0352973681855
|
||||
92 91.0 -5.34809011465 -0.0351922465446
|
||||
93 92.0 -5.31298732458 -0.0349986814067
|
||||
94 93.0 -5.27812185824 -0.034717803342
|
||||
95 94.0 -5.24358038438 -0.0343509320285
|
||||
96 95.0 -5.2094481586 -0.0338995736008
|
||||
97 96.0 -5.17580883839 -0.0333654175598
|
||||
98 97.0 -5.14274430152 -0.0327503332496
|
||||
99 98.0 -5.11033446814 -0.0320563659092
|
||||
100 99.0 -5.07865712698 -0.0312857323082
|
||||
101 100.0 -5.04778776623 -0.0304408159764
|
||||
102 101.0 -5.01779940929 -0.0295241620384
|
||||
103 102.0 -4.98876245596 -0.0285384716647
|
||||
104 103.0 -4.96074452928 -0.0274865961525
|
||||
105 104.0 -4.93381032851 -0.0263715306507
|
||||
106 105.0 -4.90802148862 -0.0251964075427
|
||||
107 106.0 -4.88343644644 -0.0239644895038
|
||||
108 107.0 -4.86011031397 -0.0226791622487
|
||||
109 108.0 -4.83809475914 -0.0213439269874
|
||||
110 109.0 -4.81743789414 -0.0199623926068
|
||||
111 110.0 -4.79818417182 -0.0185382675969
|
||||
112 111.0 -4.78037429015 -0.0170753517415
|
||||
113 112.0 -4.76404510526 -0.0155775275918
|
||||
114 113.0 -4.74922955293 -0.0140487517461
|
||||
115 114.0 -4.73595657904 -0.0124930459538
|
||||
116 115.0 -4.7242510789 -0.0109144880672
|
||||
117 116.0 -4.71413384576 -0.00931720286182
|
||||
118 117.0 -4.70562152846 -0.00770535274772
|
||||
119 118.0 -4.69872659855 -0.00608312839491
|
||||
120 119.0 -4.69345732669 -0.00445473929448
|
||||
121 120.0 -4.6898177686 -0.00282440427898
|
||||
122 121.0 -4.68780776044 -0.00119634202478
|
||||
123 122.0 -4.68742292374 0.000425238440527
|
||||
124 123.0 -4.68865467977 0.0020361472029
|
||||
125 124.0 -4.69149027336 0.00363222287571
|
||||
126 125.0 -4.69591280613 0.00520934194008
|
||||
127 126.0 -4.70190127895 0.0067634279891
|
||||
128 127.0 -4.70943064365 0.00829046085365
|
||||
129 128.0 -4.71847186379 0.00978648558781
|
||||
130 129.0 -4.72899198423 0.0112476212922
|
||||
131 130.0 -4.74095420961 0.0126700697544
|
||||
132 131.0 -4.7543179912 0.0140501238848
|
||||
133 132.0 -4.76903912216 0.0153841759291
|
||||
134 133.0 -4.78506984093 0.0166687254364
|
||||
135 134.0 -4.80235894235 0.0179003869651
|
||||
136 135.0 -4.82085189642 0.0190758975074
|
||||
137 136.0 -4.84049097437 0.0201921236154
|
||||
138 137.0 -4.86121538156 0.0212460682116
|
||||
139 138.0 -4.88296139722 0.0222348770682
|
||||
140 139.0 -4.90566252032 0.0231558449399
|
||||
141 140.0 -4.9292496215 0.0240064213355
|
||||
142 141.0 -4.95365110055 0.0247842159162
|
||||
143 142.0 -4.97879304911 0.0254870035063
|
||||
144 143.0 -5.00459941816 0.0261127287073
|
||||
145 144.0 -5.03099218995 0.0266595101027
|
||||
146 145.0 -5.05789155387 0.0271256440463
|
||||
147 146.0 -5.08521608601 0.0275096080241
|
||||
148 147.0 -5.11288293171 0.0278100635833
|
||||
149 148.0 -5.14080799097 0.0280258588231
|
||||
150 149.0 -5.16890610603 0.0281560304409
|
||||
151 150.0 -5.19709125082 0.0281998053314
|
||||
152 151.0 -5.22527672173 0.0281566017347
|
||||
153 152.0 -5.25337532941 0.0280260299338
|
||||
154 153.0 -5.28129959092 0.0278078924984
|
||||
155 154.0 -5.30896192196 0.0275021840788
|
||||
156 155.0 -5.33627482866 0.0271090907491
|
||||
157 156.0 -5.36315109852 0.0266289889046
|
||||
158 157.0 -5.38950398994 0.026062443717
|
||||
159 158.0 -5.41524742011 0.0254102071518
|
||||
160 159.0 -5.44029615055 0.0246732155563
|
||||
161 160.0 -5.46456597019 0.0238525868232
|
||||
162 161.0 -5.48797387528 0.0229496171403
|
||||
163 162.0 -5.51043824587 0.0219657773349
|
||||
164 163.0 -5.53187901853 0.0209027088232
|
||||
165 164.0 -5.55221785468 0.0197622191769
|
||||
166 165.0 -5.57137830441 0.0185462773191
|
||||
167 166.0 -5.58928596528 0.0172570083629
|
||||
168 167.0 -5.60586863576 0.0158966881068
|
||||
169 168.0 -5.62105646307 0.0144677372016
|
||||
170 169.0 -5.63478208493 0.0129727150063
|
||||
171 170.0 -5.64698076513 0.0114143131467
|
||||
172 171.0 -5.65759052241 0.00979534879707
|
||||
173 172.0 -5.66655225257 0.00811875770075
|
||||
174 173.0 -5.67380984344 0.00638758694863
|
||||
175 174.0 -5.67931028251 0.00460498753534
|
||||
176 175.0 -5.68300375706 0.00277420671195
|
||||
177 176.0 -5.68484374646 0.000898580155594
|
||||
178 177.0 -5.68478710669 -0.00101847602368
|
||||
179 178.0 -5.68279414663 -0.00297347341791
|
||||
180 179.0 -5.67882869631 -0.00496285957718
|
||||
181 180.0 -5.67285816674 -0.00698302636509
|
||||
182 181.0 -5.6648536014 -0.00903031839234
|
||||
183 182.0 -5.65478971926 -0.0111010415069
|
||||
184 183.0 -5.64264494925 -0.0131914713189
|
||||
185 184.0 -5.62840145627 -0.0152978617389
|
||||
186 185.0 -5.6120451586 -0.017416453508
|
||||
187 186.0 -5.59356573683 -0.0195434826976
|
||||
188 187.0 -5.57295663425 -0.0216751891584
|
||||
189 188.0 -5.55021504898 -0.0238078248974
|
||||
190 189.0 -5.52534191754 -0.0259376623617
|
||||
191 190.0 -5.4983418904 -0.0280610026087
|
||||
192 191.0 -5.46922329932 -0.0301741833429
|
||||
193 192.0 -5.43799811672 -0.0322735868002
|
||||
194 193.0 -5.40468190731 -0.0343556474589
|
||||
195 194.0 -5.36929377207 -0.0364168595607
|
||||
196 195.0 -5.33185628476 -0.0384537844225
|
||||
197 196.0 -5.29239542138 -0.0404630575223
|
||||
198 197.0 -5.25094048245 -0.0424413953416
|
||||
199 198.0 -5.20752400881 -0.0443856019501
|
||||
200 199.0 -5.16218169074 -0.0462925753151
|
||||
201 200.0 -5.11495227114 -0.0481593133234
|
||||
202 201.0 -5.06587744261 -0.0499829195012
|
||||
203 202.0 -5.01500173918 -0.0517606084187
|
||||
204 203.0 -4.96237242264 -0.0534897107689
|
||||
205 204.0 -4.90803936404 -0.055167678109
|
||||
206 205.0 -4.85205492059 -0.0567920872546
|
||||
207 206.0 -4.79447380837 -0.0583606443179
|
||||
208 207.0 -4.73535297113 -0.0598711883816
|
||||
209 208.0 -4.6747514457 -0.0613216948024
|
||||
210 209.0 -4.61273022413 -0.0627102781377
|
||||
211 210.0 -4.54935211328 -0.0640351946902
|
||||
212 211.0 -4.4846815919 -0.0652948446678
|
||||
213 212.0 -4.41878466581 -0.0664877739558
|
||||
214 213.0 -4.35172872155 -0.0676126754981
|
||||
215 214.0 -4.28358237872 -0.0686683902899
|
||||
216 215.0 -4.21441534165 -0.0696539079796
|
||||
217 216.0 -4.14429825061 -0.070568367083
|
||||
218 217.0 -4.07330253293 -0.0714110548116
|
||||
219 218.0 -4.00150025463 -0.0721814065199
|
||||
220 219.0 -3.92896397266 -0.072879004774
|
||||
221 220.0 -3.85576658834 -0.0735035780505
|
||||
222 221.0 -3.78198120223 -0.0740549990687
|
||||
223 222.0 -3.70768097086 -0.0745332827669
|
||||
224 223.0 -3.63293896573 -0.0749385839297
|
||||
225 224.0 -3.5578280347 -0.0752711944755
|
||||
226 225.0 -3.48242066643 -0.075531540416
|
||||
227 226.0 -3.4067888579 -0.0757201784978
|
||||
228 227.0 -3.33100398548 -0.0758377925383
|
||||
229 228.0 -3.25513667985 -0.0758851894693
|
||||
230 229.0 -3.17925670492 -0.0758632951011
|
||||
231 230.0 -3.10343284123 -0.0757731496217
|
||||
232 231.0 -3.02773277394 -0.0756159028468
|
||||
233 232.0 -2.95222298559 -0.0753928092342
|
||||
234 233.0 -2.87696865416 -0.0751052226812
|
||||
235 234.0 -2.80203355622 -0.0747545911191
|
||||
236 235.0 -2.72747997572 -0.0743424509249
|
||||
237 236.0 -2.65336861841 -0.073870421164
|
||||
238 237.0 -2.57975853208 -0.0733401976859
|
||||
239 238.0 -2.50670703279 -0.0727535470871
|
||||
240 239.0 -2.4342696372 -0.0721123005638
|
||||
241 240.0 -2.36250000104 -0.0714183476691
|
||||
242 241.0 -2.29144986396 -0.0706736299971
|
||||
243 242.0 -2.22116900065 -0.0698801348102
|
||||
244 243.0 -2.15170517837 -0.0690398886302
|
||||
245 244.0 -2.0831041209 -0.0681549508121
|
||||
246 245.0 -2.01540947892 -0.067227407119
|
||||
247 246.0 -1.94866280684 -0.0662593633171
|
||||
248 247.0 -1.88290354594 -0.0652529388105
|
||||
249 248.0 -1.81816901389 -0.0642102603325
|
||||
250 249.0 -1.7544944006 -0.0631334557138
|
||||
251 250.0 -1.69191277013 -0.0620246477436
|
||||
252 251.0 -1.6304550688 -0.0608859481423
|
||||
253 252.0 -1.57015013921 -0.059719451663
|
||||
254 253.0 -1.51102474011 -0.0585272303374
|
||||
255 254.0 -1.45310357187 -0.0573113278834
|
||||
256 255.0 -1.39640930762 -0.0560737542899
|
||||
257 256.0 -1.34096262951 -0.054816480593
|
||||
258 257.0 -1.28678227024 -0.0535414338587
|
||||
259 258.0 -1.23388505944 -0.0522504923856
|
||||
260 259.0 -1.18228597475 -0.0509454811405
|
||||
261 260.0 -1.13199819729 -0.0496281674395
|
||||
262 261.0 -1.08303317143 -0.0483002568854
|
||||
263 262.0 -1.03540066834 -0.046963389572
|
||||
264 263.0 -0.989108853377 -0.0456191365664
|
||||
265 264.0 -0.944164356669 -0.0442689966762
|
||||
266 265.0 -0.900572346917 -0.0429143935113
|
||||
267 266.0 -0.858336607922 -0.0415566728462
|
||||
268 267.0 -0.817459617608 -0.0401971002897
|
||||
269 268.0 -0.777942629232 -0.0388368592669
|
||||
270 269.0 -0.739785754436 -0.0374770493178
|
||||
271 270.0 -0.702988047855 -0.0361186847156
|
||||
272 271.0 -0.667547592939 -0.0347626934072
|
||||
273 272.0 -0.633461588675 -0.0334099162773
|
||||
274 273.0 -0.600726436882 -0.0320611067354
|
||||
275 274.0 -0.569337829756 -0.0307169306269
|
||||
276 275.0 -0.539290837348 -0.0293779664649
|
||||
277 276.0 -0.510579994645 -0.0280447059807
|
||||
278 277.0 -0.483199387947 -0.0267175549897
|
||||
279 278.0 -0.457142740217 -0.0253968345674
|
||||
280 279.0 -0.432403495111 -0.0240827825309
|
||||
281 280.0 -0.408974899365 -0.0227755552188
|
||||
282 281.0 -0.386850083265 -0.0214752295619
|
||||
283 282.0 -0.366022138902 -0.020181805438
|
||||
284 283.0 -0.346484195932 -0.0188952082997
|
||||
285 284.0 -0.328229494574 -0.0176152920667
|
||||
286 285.0 -0.311251455597 -0.0163418422722
|
||||
287 286.0 -0.295543747024 -0.0150745794496
|
||||
288 287.0 -0.28110034735 -0.0138131627512
|
||||
289 288.0 -0.267915605017 -0.0125571937823
|
||||
290 289.0 -0.255984293962 -0.011306220639
|
||||
291 290.0 -0.245301665026 -0.0100597421363
|
||||
292 291.0 -0.235863493049 -0.00881721220956
|
||||
293 292.0 -0.22766611948 -0.00757804447631
|
||||
294 293.0 -0.220706490355 -0.00634161694135
|
||||
295 294.0 -0.214982189503 -0.00510727682957
|
||||
296 295.0 -0.210491466861 -0.00387434552992
|
||||
297 296.0 -0.207233261801 -0.00264212363344
|
||||
298 297.0 -0.205207221373 -0.00140989604849
|
||||
299 298.0 -0.204413713408 -0.00017693717569
|
||||
300 299.0 -0.204853834414 0.0010574838751
|
||||
301 300.0 -0.206529412255 0.00229409804323
|
||||
302 301.0 -0.209443003569 0.00353363106913
|
||||
303 302.0 -0.213597885954 0.00477679825726
|
||||
304 303.0 -0.218998044922 0.00602429926791
|
||||
305 304.0 -0.22564815567 0.00727681295572
|
||||
306 305.0 -0.23355355972 0.00853499227222
|
||||
307 306.0 -0.2427202365 0.00979945924997
|
||||
308 307.0 -0.253154769958 0.0110708000854
|
||||
309 308.0 -0.264864310313 0.0123495603372
|
||||
310 309.0 -0.277856531075 0.0136362402565
|
||||
311 310.0 -0.292139581459 0.0149312902659
|
||||
312 311.0 -0.307722034364 0.0162351066015
|
||||
313 312.0 -0.324612830087 0.0175480271349
|
||||
314 313.0 -0.342821215943 0.0188703273888
|
||||
315 314.0 -0.362356682012 0.0202022167596
|
||||
316 315.0 -0.383228893218 0.0215438349636
|
||||
317 316.0 -0.405447617967 0.0228952487148
|
||||
318 317.0 -0.429022653586 0.0242564486517
|
||||
319 318.0 -0.45396374882 0.0256273465206
|
||||
320 319.0 -0.480280523637 0.0270077726275
|
||||
321 320.0 -0.507982386639 0.0283974735696
|
||||
322 321.0 -0.537078450328 0.029796110253
|
||||
323 322.0 -0.567577444555 0.0312032562068
|
||||
324 323.0 -0.59948762842 0.0326183962009
|
||||
325 324.0 -0.632816700956 0.0340409251716
|
||||
326 325.0 -0.667571710883 0.0354701474639
|
||||
327 326.0 -0.703758965776 0.0369052763923
|
||||
328 327.0 -0.741383940946 0.038345434125
|
||||
329 328.0 -0.780451188376 0.0397896518935
|
||||
330 329.0 -0.820964246018 0.0412368705304
|
||||
331 330.0 -0.862925547807 0.042685941334
|
||||
332 331.0 -0.906336334692 0.0441356272615
|
||||
333 332.0 -0.951196567028 0.045584604448
|
||||
334 333.0 -0.997504838648 0.0470314640498
|
||||
335 334.0 -1.04525829294 0.048474714408
|
||||
336 335.0 -1.09445254125 0.0499127835288
|
||||
337 336.0 -1.1450815839 0.0513440218749
|
||||
338 337.0 -1.1971377342 0.0527667054614
|
||||
339 338.0 -1.25061154564 0.0541790392498
|
||||
340 339.0 -1.30549174267 0.0555791608316
|
||||
341 340.0 -1.36176515529 0.0569651443923
|
||||
342 341.0 -1.41941665773 0.0583350049463
|
||||
343 342.0 -1.47842911151 0.0596867028317
|
||||
344 343.0 -1.53878331313 0.061018148454
|
||||
345 344.0 -1.60045794659 0.0623272072653
|
||||
346 345.0 -1.66342954101 0.0636117049668
|
||||
347 346.0 -1.72767243359 0.0648694329207
|
||||
348 347.0 -1.79315873807 0.0660981537565
|
||||
349 348.0 -1.85985831882 0.0672956071568
|
||||
350 349.0 -1.92773877092 0.0684595158069
|
||||
351 350.0 -1.99676540616 0.0695875914917
|
||||
352 351.0 -2.06690124527 0.0706775413231
|
||||
353 352.0 -2.13810701636 0.0717270740805
|
||||
354 353.0 -2.21034115987 0.0727339066469
|
||||
355 354.0 -2.28355983986 0.0736957705223
|
||||
356 355.0 -2.35771696194 0.0746104183955
|
||||
357 356.0 -2.43276419776 0.0754756307561
|
||||
358 357.0 -2.50865101613 0.0762892225281
|
||||
359 358.0 -2.58532472075 0.0770490497051
|
||||
360 359.0 -2.66273049463 0.0777530159679
|
||||
|
||||
# Table of the potential and its negative derivative for frustrated beta sheet
|
||||
# (Note: Derivatives are in units of energy/radians, not energy/degrees.)
|
||||
# ./calc_dihedral_table.py 5.6 57.29577951308232 6 6.0 180 6 0.0 359 360
|
||||
|
||||
FRUSTRATED_BETA
|
||||
N 360 DEGREES
|
||||
|
||||
1 0.0 -2.55809068762 0.0731724739818
|
||||
2 1.0 -2.63154144494 0.0737195744566
|
||||
3 2.0 -2.70551060968 0.0742089966437
|
||||
4 3.0 -2.77993963883 0.074639023134
|
||||
5 4.0 -2.85476830901 0.0750080115297
|
||||
6 5.0 -2.92993479441 0.0753144003899
|
||||
7 6.0 -3.00537575069 0.0755567150326
|
||||
8 7.0 -3.08102640456 0.0757335731758
|
||||
9 8.0 -3.15682064892 0.0758436903983
|
||||
10 9.0 -3.23269114341 0.075885885404
|
||||
11 10.0 -3.30856942003 0.0758590850738
|
||||
12 11.0 -3.38438599377 0.0757623292865
|
||||
13 12.0 -3.46007047791 0.0755947754951
|
||||
14 13.0 -3.53555170381 0.0753557030426
|
||||
15 14.0 -3.61075784476 0.0750445172025
|
||||
16 15.0 -3.68561654392 0.0746607529305
|
||||
17 16.0 -3.76005504566 0.0742040783151
|
||||
18 17.0 -3.83400033034 0.0736742977129
|
||||
19 18.0 -3.907379252 0.0730713545594
|
||||
20 19.0 -3.98011867868 0.0723953338429
|
||||
21 20.0 -4.0521456351 0.0716464642332
|
||||
22 21.0 -4.12338744726 0.0708251198546
|
||||
23 22.0 -4.19377188857 0.0699318216967
|
||||
24 23.0 -4.26322732737 0.0689672386556
|
||||
25 24.0 -4.33168287509 0.0679321881993
|
||||
26 25.0 -4.39906853508 0.0668276366524
|
||||
27 26.0 -4.46531535141 0.0656546990963
|
||||
28 27.0 -4.53035555742 0.0644146388823
|
||||
29 28.0 -4.59412272358 0.0631088667546
|
||||
30 29.0 -4.65655190431 0.061738939584
|
||||
31 30.0 -4.71757978327 0.0603065587109
|
||||
32 31.0 -4.77714481686 0.0588135679005
|
||||
33 32.0 -4.83518737548 0.057261950911
|
||||
34 33.0 -4.89164988211 0.0556538286799
|
||||
35 34.0 -4.94647694795 0.0539914561312
|
||||
36 35.0 -4.99961550465 0.0522772186102
|
||||
37 36.0 -5.05101493277 0.0505136279528
|
||||
38 37.0 -5.10062718621 0.048703318195
|
||||
39 38.0 -5.14840691207 0.0468490409338
|
||||
40 39.0 -5.19431156578 0.0449536603471
|
||||
41 40.0 -5.23830152101 0.0430201478838
|
||||
42 41.0 -5.28034017422 0.0410515766363
|
||||
43 42.0 -5.3203940433 0.0390511154063
|
||||
44 43.0 -5.35843286021 0.0370220224793
|
||||
45 44.0 -5.39442965726 0.0349676391193
|
||||
46 45.0 -5.4283608467 0.0328913828015
|
||||
47 46.0 -5.46020629342 0.0307967401964
|
||||
48 47.0 -5.48994938059 0.028687259923
|
||||
49 48.0 -5.51757706789 0.0265665450883
|
||||
50 49.0 -5.54307994213 0.0244382456298
|
||||
51 50.0 -5.56645226024 0.0223060504811
|
||||
52 51.0 -5.58769198425 0.0201736795783
|
||||
53 52.0 -5.60680080825 0.0180448757265
|
||||
54 53.0 -5.62378417713 0.0159233963481
|
||||
55 54.0 -5.63865129702 0.0138130051308
|
||||
56 55.0 -5.6514151374 0.0117174635982
|
||||
57 56.0 -5.66209242462 0.00964052262251
|
||||
58 57.0 -5.67070362704 0.00758591390103
|
||||
59 58.0 -5.67727293157 0.00555734141841
|
||||
60 59.0 -5.6818282117 0.00355847291538
|
||||
61 60.0 -5.68440098698 0.00159293138608
|
||||
62 61.0 -5.68502637408 -0.000335713374531
|
||||
63 62.0 -5.68374302934 -0.00222395315148
|
||||
64 63.0 -5.68059308309 -0.0040683495974
|
||||
65 64.0 -5.67562206565 -0.00586554240548
|
||||
66 65.0 -5.66887882528 -0.00761225734683
|
||||
67 66.0 -5.66041543813 -0.00930531415106
|
||||
68 67.0 -5.65028711044 -0.0109416342099
|
||||
69 68.0 -5.63855207307 -0.0125182480831
|
||||
70 69.0 -5.6252714687 -0.0140323027883
|
||||
71 70.0 -5.61050923182 -0.0154810688529
|
||||
72 71.0 -5.59433196178 -0.0168619471125
|
||||
73 72.0 -5.57680878923 -0.0181724752358
|
||||
74 73.0 -5.5580112361 -0.019410333958
|
||||
75 74.0 -5.53801306959 -0.0205733530082
|
||||
76 75.0 -5.51689015031 -0.0216595167121
|
||||
77 76.0 -5.49472027505 -0.0226669692568
|
||||
78 77.0 -5.47158301441 -0.0235940196022
|
||||
79 78.0 -5.44755954575 -0.0244391460249
|
||||
80 79.0 -5.42273248172 -0.0252010002837
|
||||
81 80.0 -5.3971856949 -0.0258784113929
|
||||
82 81.0 -5.37100413881 -0.0264703889936
|
||||
83 82.0 -5.34427366574 -0.0269761263135
|
||||
84 83.0 -5.31708084192 -0.0273950027051
|
||||
85 84.0 -5.28951276022 -0.0277265857564
|
||||
86 85.0 -5.26165685114 -0.0279706329651
|
||||
87 86.0 -5.23360069216 -0.0281270929735
|
||||
88 87.0 -5.20543181621 -0.0281961063563
|
||||
89 88.0 -5.17723751951 -0.0281780059613
|
||||
90 89.0 -5.14910466934 -0.0280733167983
|
||||
91 90.0 -5.12111951208 -0.0278827554757
|
||||
92 91.0 -5.09336748214 -0.0276072291861
|
||||
93 92.0 -5.06593301201 -0.0272478342399
|
||||
94 93.0 -5.0388993441 -0.026805854151
|
||||
95 94.0 -5.01234834466 -0.0262827572773
|
||||
96 95.0 -4.98636032033 -0.0256801940208
|
||||
97 96.0 -4.96101383762 -0.0249999935924
|
||||
98 97.0 -4.93638554598 -0.0242441603499
|
||||
99 98.0 -4.91255000457 -0.0234148697145
|
||||
100 99.0 -4.88957951348 -0.0225144636776
|
||||
101 100.0 -4.86754394953 -0.0215454459053
|
||||
102 101.0 -4.84651060724 -0.0205104764546
|
||||
103 102.0 -4.8265440452 -0.01941236611
|
||||
104 103.0 -4.80770593836 -0.0182540703564
|
||||
105 104.0 -4.79005493648 -0.0170386830008
|
||||
106 105.0 -4.77364652914 -0.0157694294583
|
||||
107 106.0 -4.7585329176 -0.0144496597171
|
||||
108 107.0 -4.74476289391 -0.0130828410011
|
||||
109 108.0 -4.73238172744 -0.0116725501446
|
||||
110 109.0 -4.72143105919 -0.0102224657007
|
||||
111 110.0 -4.71194880414 -0.00873635979846
|
||||
112 111.0 -4.70396906182 -0.0072180897712
|
||||
113 112.0 -4.69752203541 -0.00567158957449
|
||||
114 113.0 -4.69263395945 -0.00410086101469
|
||||
115 114.0 -4.68932703648 -0.00250996480925
|
||||
116 115.0 -4.68761938265 -0.000903011500147
|
||||
117 116.0 -4.68752498248 0.00071584775762
|
||||
118 117.0 -4.68905365291 0.00234243051027
|
||||
119 118.0 -4.69221101668 0.00397253239976
|
||||
120 119.0 -4.69699848518 0.00560193661579
|
||||
121 120.0 -4.70341325069 0.00722642338265
|
||||
122 121.0 -4.71144828821 0.00884177945771
|
||||
123 122.0 -4.72109236669 0.0104438076188
|
||||
124 123.0 -4.73233006984 0.0120283361174
|
||||
125 124.0 -4.74514182625 0.0135912280748
|
||||
126 125.0 -4.75950394898 0.0151283907985
|
||||
127 126.0 -4.77538868431 0.0166357849963
|
||||
128 127.0 -4.79276426974 0.0181094338658
|
||||
129 128.0 -4.81159500092 0.0195454320375
|
||||
130 129.0 -4.83184130754 0.0209399543498
|
||||
131 130.0 -4.8534598378 0.0222892644342
|
||||
132 131.0 -4.87640355143 0.0235897230915
|
||||
133 132.0 -4.90062182095 0.0248377964369
|
||||
134 133.0 -4.92606054096 0.0260300637961
|
||||
135 134.0 -4.95266224518 0.0271632253326
|
||||
136 135.0 -4.98036623096 0.028234109388
|
||||
137 136.0 -5.00910869107 0.0292396795182
|
||||
138 137.0 -5.03882285221 0.0301770412082
|
||||
139 138.0 -5.06943912022 0.0310434482505
|
||||
140 139.0 -5.10088523142 0.0318363087705
|
||||
141 140.0 -5.13308640979 0.0325531908865
|
||||
142 141.0 -5.16596552963 0.0331918279898
|
||||
143 142.0 -5.19944328334 0.0337501236332
|
||||
144 143.0 -5.23343835383 0.0342261560164
|
||||
145 144.0 -5.26786759123 0.0346181820585
|
||||
146 145.0 -5.30264619353 0.0349246410472
|
||||
147 146.0 -5.33768789051 0.0351441578585
|
||||
148 147.0 -5.37290513082 0.0352755457383
|
||||
149 148.0 -5.40820927152 0.0353178086401
|
||||
150 149.0 -5.4435107698 0.0352701431151
|
||||
151 150.0 -5.4787193763 0.0351319397498
|
||||
152 151.0 -5.51374432971 0.0349027841491
|
||||
153 152.0 -5.54849455206 0.0345824574643
|
||||
154 153.0 -5.58287884436 0.0341709364636
|
||||
155 154.0 -5.61680608206 0.0336683931487
|
||||
156 155.0 -5.65018540988 0.0330751939177
|
||||
157 156.0 -5.68292643563 0.0323918982779
|
||||
158 157.0 -5.71493942249 0.0316192571138
|
||||
159 158.0 -5.74613547931 0.0307582105139
|
||||
160 159.0 -5.77642674856 0.029809885165
|
||||
161 160.0 -5.80572659147 0.0287755913197
|
||||
162 161.0 -5.83394976986 0.0276568193473
|
||||
163 162.0 -5.86101262442 0.0264552358763
|
||||
164 163.0 -5.8868332488 0.025172679541
|
||||
165 164.0 -5.91133165941 0.0238111563427
|
||||
166 165.0 -5.93442996024 0.0223728346376
|
||||
167 166.0 -5.95605250261 0.0208600397671
|
||||
168 167.0 -5.97612603931 0.0192752483425
|
||||
169 168.0 -5.99457987285 0.0176210822011
|
||||
170 169.0 -6.01134599757 0.015900302049
|
||||
171 170.0 -6.02635923519 0.014115800807
|
||||
172 171.0 -6.03955736358 0.0122705966784
|
||||
173 172.0 -6.05088123845 0.0103678259555
|
||||
174 173.0 -6.0602749078 0.00841073558436
|
||||
175 174.0 -6.06768571866 0.00640267550713
|
||||
176 175.0 -6.0730644163 0.00434709080102
|
||||
177 176.0 -6.07636523524 0.00224751363529
|
||||
178 177.0 -6.07754598232 0.000107555066143
|
||||
179 178.0 -6.07656811141 -0.00206910330914
|
||||
180 179.0 -6.07339678973 -0.00427871781763
|
||||
181 180.0 -6.06800095563 -0.00651749127408
|
||||
182 181.0 -6.06035336781 -0.00878158162059
|
||||
183 182.0 -6.05043064586 -0.0110671106207
|
||||
184 183.0 -6.03821330204 -0.0133701725859
|
||||
185 184.0 -6.02368576439 -0.0156868431131
|
||||
186 185.0 -6.00683639108 -0.0180131878107
|
||||
187 186.0 -5.98765747603 -0.0203452709919
|
||||
188 187.0 -5.96614524589 -0.0226791643135
|
||||
189 188.0 -5.94229984843 -0.025010955339
|
||||
190 189.0 -5.91612533236 -0.0273367560054
|
||||
191 190.0 -5.88762961878 -0.0296527109716
|
||||
192 191.0 -5.85682446433 -0.0319550058299
|
||||
193 192.0 -5.82372541626 -0.0342398751598
|
||||
194 193.0 -5.78835175943 -0.0365036104045
|
||||
195 194.0 -5.75072645562 -0.0387425675516
|
||||
196 195.0 -5.71087607524 -0.0409531746008
|
||||
197 196.0 -5.66883072166 -0.0431319387984
|
||||
198 197.0 -5.62462394846 -0.0452754536249
|
||||
199 198.0 -5.57829266983 -0.0473804055171
|
||||
200 199.0 -5.5298770643 -0.0494435803104
|
||||
201 200.0 -5.47942047235 -0.0514618693867
|
||||
202 201.0 -5.42696928781 -0.0534322755136
|
||||
203 202.0 -5.37257284377 -0.055351918363
|
||||
204 203.0 -5.316283293 -0.0572180396955
|
||||
205 204.0 -5.25815548345 -0.059028008202
|
||||
206 205.0 -5.19824682901 -0.0607793239895
|
||||
207 206.0 -5.13661717604 -0.0624696227052
|
||||
208 207.0 -5.0733286659 -0.0640966792879
|
||||
209 208.0 -5.00844559393 -0.0656584113417
|
||||
210 209.0 -4.94203426529 -0.0671528821253
|
||||
211 210.0 -4.87416284794 -0.0685783031513
|
||||
212 211.0 -4.80490122327 -0.0699330363936
|
||||
213 212.0 -4.7343208347 -0.0712155960973
|
||||
214 213.0 -4.66249453466 -0.0724246501921
|
||||
215 214.0 -4.58949643037 -0.0735590213066
|
||||
216 215.0 -4.51540172879 -0.0746176873849
|
||||
217 216.0 -4.44028658118 -0.0755997819067
|
||||
218 217.0 -4.3642279276 -0.0765045937139
|
||||
219 218.0 -4.28730334182 -0.0773315664459
|
||||
220 219.0 -4.20959087694 -0.0780802975905
|
||||
221 220.0 -4.13116891218 -0.0787505371538
|
||||
222 221.0 -4.0521160012 -0.0793421859574
|
||||
223 222.0 -3.97251072229 -0.0798552935693
|
||||
224 223.0 -3.89243153076 -0.0802900558785
|
||||
225 224.0 -3.81195661404 -0.0806468123209
|
||||
226 225.0 -3.73116374964 -0.0809260427693
|
||||
227 226.0 -3.65013016636 -0.0811283640964
|
||||
228 227.0 -3.56893240921 -0.0812545264246
|
||||
229 228.0 -3.48764620813 -0.0813054090744
|
||||
230 229.0 -3.4063463509 -0.0812820162266
|
||||
231 230.0 -3.32510656064 -0.0811854723104
|
||||
232 231.0 -3.24399937793 -0.081017017134
|
||||
233 232.0 -3.16309604794 -0.0807780007742
|
||||
234 233.0 -3.08246641287 -0.0804698782381
|
||||
235 234.0 -3.00217880976 -0.0800942039176
|
||||
236 235.0 -2.92229997393 -0.079652625851
|
||||
237 236.0 -2.84289494829 -0.0791468798106
|
||||
238 237.0 -2.76402699866 -0.0785787832348
|
||||
239 238.0 -2.68575753514 -0.0779502290223
|
||||
240 239.0 -2.60814603984 -0.077263179207
|
||||
241 240.0 -2.53125000097 -0.0765196585342
|
||||
242 241.0 -2.4551248533 -0.0757217479546
|
||||
243 242.0 -2.37982392531 -0.0748715780578
|
||||
244 243.0 -2.30539839282 -0.073971322463
|
||||
245 244.0 -2.23189723927 -0.0730231911866
|
||||
246 245.0 -2.15936722267 -0.072029424007
|
||||
247 246.0 -2.0878528491 -0.0709922838436
|
||||
248 247.0 -2.01739635293 -0.0699140501714
|
||||
249 248.0 -1.94803768347 -0.0687970124882
|
||||
250 249.0 -1.87981449824 -0.0676434638537
|
||||
251 250.0 -1.81276216256 -0.0664556945194
|
||||
252 251.0 -1.74691375554 -0.0652359856651
|
||||
253 252.0 -1.68230008218 -0.0639866032624
|
||||
254 253.0 -1.61894969164 -0.0627097920793
|
||||
255 254.0 -1.55688890134 -0.0614077698443
|
||||
256 255.0 -1.49614182687 -0.0600827215855
|
||||
257 256.0 -1.43673041741 -0.05873679416
|
||||
258 257.0 -1.37867449659 -0.0573720909874
|
||||
259 258.0 -1.32199180845 -0.0559906670036
|
||||
260 259.0 -1.26669806833 -0.0545945238457
|
||||
261 260.0 -1.21280701853 -0.0531856052829
|
||||
262 261.0 -1.1603304883 -0.0517657929031
|
||||
263 262.0 -1.1092784581 -0.0503369020679
|
||||
264 263.0 -1.05965912771 -0.0489006781451
|
||||
265 264.0 -1.01147898802 -0.0474587930279
|
||||
266 265.0 -0.964742896092 -0.0460128419505
|
||||
267 266.0 -0.919454153297 -0.0445643406057
|
||||
268 267.0 -0.875614586172 -0.0431147225719
|
||||
269 268.0 -0.833224629688 -0.0416653370554
|
||||
270 269.0 -0.792283412613 -0.0402174469521
|
||||
271 270.0 -0.752788844664 -0.038772227232
|
||||
272 271.0 -0.714737705101 -0.0373307636499
|
||||
273 272.0 -0.67812573245 -0.0358940517831
|
||||
274 273.0 -0.642947715028 -0.0344629963972
|
||||
275 274.0 -0.609197581934 -0.0330384111393
|
||||
276 275.0 -0.576868494182 -0.0316210185584
|
||||
277 276.0 -0.545952935658 -0.0302114504483
|
||||
278 277.0 -0.51644280357 -0.0288102485125
|
||||
279 278.0 -0.488329498068 -0.0274178653447
|
||||
280 279.0 -0.461604010741 -0.0260346657211
|
||||
281 280.0 -0.436257011655 -0.0246609281969
|
||||
282 281.0 -0.412278934657 -0.023296847002
|
||||
283 282.0 -0.389660060626 -0.0219425342253
|
||||
284 283.0 -0.368390598407 -0.0205980222818
|
||||
285 284.0 -0.348460763137 -0.01926326665
|
||||
286 285.0 -0.329860851704 -0.0179381488715
|
||||
287 286.0 -0.312581315078 -0.0166224797996
|
||||
288 287.0 -0.296612827279 -0.015316003087
|
||||
289 288.0 -0.281946350734 -0.0140183988977
|
||||
290 289.0 -0.268573197826 -0.0127292878319
|
||||
291 290.0 -0.256485088408 -0.0114482350481
|
||||
292 291.0 -0.245674203109 -0.0101747545698
|
||||
293 292.0 -0.236133232246 -0.00890831375923
|
||||
294 293.0 -0.227855420178 -0.00764833794542
|
||||
295 294.0 -0.220834604976 -0.00639421518813
|
||||
296 295.0 -0.215065253253 -0.00514530116277
|
||||
297 296.0 -0.210542490065 -0.00390092414876
|
||||
298 297.0 -0.207262123775 -0.00266039010467
|
||||
299 298.0 -0.205220665805 -0.00142298781263
|
||||
300 299.0 -0.204415345223 -0.000187994074493
|
||||
301 300.0 -0.204844118104 0.00104532105779
|
||||
302 301.0 -0.206505671662 0.00227768903543
|
||||
303 302.0 -0.209399423126 0.0035098375675
|
||||
304 303.0 -0.213525513386 0.00474248539479
|
||||
305 304.0 -0.218884795423 0.00597633710062
|
||||
306 305.0 -0.225478817581 0.00721207797616
|
||||
307 306.0 -0.233309801737 0.00845036895769
|
||||
308 307.0 -0.242380616448 0.00969184165314
|
||||
309 308.0 -0.252694745185 0.0109370934746
|
||||
310 309.0 -0.264256249747 0.0121866828936
|
||||
311 310.0 -0.277069729013 0.0134411248358
|
||||
312 311.0 -0.291140273151 0.0147008862297
|
||||
313 312.0 -0.306473413467 0.0159663817261
|
||||
314 313.0 -0.323075068066 0.0172379696031
|
||||
315 314.0 -0.340951483513 0.018515947869
|
||||
316 315.0 -0.360109172702 0.0198005505798
|
||||
317 316.0 -0.380554849155 0.0210919443819
|
||||
318 317.0 -0.402295357987 0.0223902252933
|
||||
319 318.0 -0.425337603767 0.0236954157356
|
||||
320 319.0 -0.449688475549 0.0250074618263
|
||||
321 320.0 -0.475354769327 0.0263262309427
|
||||
322 321.0 -0.50234310819 0.0276515095659
|
||||
323 322.0 -0.530659860472 0.0289830014145
|
||||
324 323.0 -0.560311056174 0.0303203258736
|
||||
325 324.0 -0.59130230198 0.0316630167284
|
||||
326 325.0 -0.623638695141 0.0330105212056
|
||||
327 326.0 -0.657324736579 0.0343621993296
|
||||
328 327.0 -0.692364243488 0.0357173235955
|
||||
329 328.0 -0.728760261774 0.0370750789637
|
||||
330 329.0 -0.766514978659 0.0384345631765
|
||||
331 330.0 -0.805629635748 0.0397947873984
|
||||
332 331.0 -0.846104442913 0.04115467718
|
||||
333 332.0 -0.887938493289 0.042513073745
|
||||
334 333.0 -0.93112967973 0.0438687355968
|
||||
335 334.0 -0.975674613021 0.0452203404434
|
||||
336 335.0 -1.02156854218 0.0465664874361
|
||||
337 336.0 -1.06880527714 0.0479056997168
|
||||
338 337.0 -1.11737711415 0.0492364272675
|
||||
339 338.0 -1.16727476416 0.0505570500574
|
||||
340 339.0 -1.2184872845 0.051865881477
|
||||
341 340.0 -1.27100201415 0.0531611720525
|
||||
342 341.0 -1.32480451282 0.0544411134304
|
||||
343 342.0 -1.37987850417 0.055703842622
|
||||
344 343.0 -1.43620582346 0.0569474464963
|
||||
345 344.0 -1.49376636966 0.0581699665097
|
||||
346 345.0 -1.55253806258 0.05936940366
|
||||
347 346.0 -1.61249680493 0.0605437236497
|
||||
348 347.0 -1.67361644969 0.0616908622471
|
||||
349 348.0 -1.73586877296 0.0628087308273
|
||||
350 349.0 -1.79922345238 0.0638952220804
|
||||
351 350.0 -1.86364805137 0.0649482158688
|
||||
352 351.0 -1.92910800931 0.0659655852184
|
||||
353 352.0 -1.9955666377 0.066945202426
|
||||
354 353.0 -2.06298512258 0.0678849452658
|
||||
355 354.0 -2.13132253309 0.0687827032771
|
||||
356 355.0 -2.20053583647 0.0696363841147
|
||||
357 356.0 -2.27057991931 0.0704439199439
|
||||
358 357.0 -2.3414076153 0.0712032738621
|
||||
359 358.0 -2.41296973939 0.0719124463259
|
||||
360 359.0 -2.48521512832 0.072569481568
|
||||
@ -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 3.4 21018.6991377 533598.403624
|
||||
62 3.405 18527.1884441 464731.50307
|
||||
63 3.41 16355.4608211 405427.532611
|
||||
64 3.415 14459.3541284 354266.400629
|
||||
65 3.42 12801.228731 310052.319542
|
||||
66 3.425 11348.9427887 271776.300627
|
||||
67 3.43 10074.9979765 238585.259865
|
||||
68 3.435 8955.82575185 209756.510836
|
||||
69 3.44 7971.18978782 184676.657916
|
||||
70 3.445 7103.68463562 162824.092297
|
||||
71 3.45 6338.31427303 143754.444665
|
||||
72 3.455 5662.13711315 127088.469763
|
||||
73 3.46 5063.9664184 112501.9356
|
||||
74 3.465 4534.11699728 99717.1686967
|
||||
75 3.47 4064.19064042 88495.970274
|
||||
76 3.475 3646.89404446 78633.6696895
|
||||
77 3.48 3275.88403311 69954.1231906
|
||||
78 3.485 2945.63575657 62305.4999784
|
||||
79 3.49 2651.33026883 55556.7252625
|
||||
80 3.495 2388.75847582 49594.4725913
|
||||
81 3.5 2154.23893796 44320.6162531
|
||||
82 3.505 1944.54741747 39650.0697323
|
||||
83 3.51 1756.8563988 35508.9486835
|
||||
84 3.515 1588.68309151 31833.0071751
|
||||
85 3.52 1437.84465949 28566.3044359
|
||||
86 3.525 1302.41961585 25660.0663588
|
||||
87 3.53 1180.71448694 23071.7118275
|
||||
88 3.535 1071.23498579 20764.0187577
|
||||
89 3.54 972.661050857 18704.4087568
|
||||
90 3.545 883.825202407 16864.3326446
|
||||
91 3.55 803.693750954 15218.7418698
|
||||
92 3.555 731.350460573 13745.6331832
|
||||
93 3.56 665.982328363 12425.6558809
|
||||
94 3.565 606.867190408 11241.7725673
|
||||
95 3.57 553.362906393 10178.9657593
|
||||
96 3.575 504.897910387 9223.98381086
|
||||
97 3.58 460.962945446 8365.12060921
|
||||
98 3.585 421.103825306 7592.02431669
|
||||
99 3.59 384.915088285 6895.53112553
|
||||
100 3.595 352.034427161 6267.5205811
|
||||
101 3.6 322.137794751 5700.78952663
|
||||
102 3.605 294.935098544 5188.94214534
|
||||
103 3.61 270.166409464 4726.29393494
|
||||
104 3.615 247.598619855 4307.78775517
|
||||
105 3.62 227.022494431 3928.92034957
|
||||
106 3.625 208.250065337 3585.67796495
|
||||
107 3.63 191.112328875 3274.47988201
|
||||
108 3.635 175.457206974 2992.12883298
|
||||
109 3.64 161.147741205 2735.76742147
|
||||
110 3.645 148.060491326 2502.83977901
|
||||
111 3.65 136.084113848 2291.05779528
|
||||
112 3.655 125.118099223 2098.37134728
|
||||
113 3.66 115.071648949 1922.94202847
|
||||
114 3.665 105.862676198 1763.11994431
|
||||
115 3.67 97.4169155884 1617.42319704
|
||||
116 3.675 89.6671295106 1484.51973131
|
||||
117 3.68 82.5523999227 1363.21125435
|
||||
118 3.685 76.0174958886 1252.41898087
|
||||
119 3.69 70.0123082899 1151.17098442
|
||||
120 3.695 64.4913441675 1058.59096449
|
||||
121 3.7 59.4132740402 973.88826227
|
||||
122 3.705 54.7405263329 896.348978842
|
||||
123 3.71 50.438923727 825.328067481
|
||||
124 3.715 46.4773568526 760.242287449
|
||||
125 3.72 42.8274912666 700.563920374
|
||||
126 3.725 39.4635041252 645.815162231
|
||||
127 3.73 36.3618473701 595.563114331
|
||||
128 3.735 33.5010346035 549.415305905
|
||||
129 3.74 30.8614491473 507.015688796
|
||||
130 3.745 28.425171059 468.041051794
|
||||
131 3.75 26.1758211241 432.197808262
|
||||
132 3.755 24.0984200646 399.21911609
|
||||
133 3.76 22.179261392 368.86229374
|
||||
134 3.765 20.4057965086 340.906500282
|
||||
135 3.77 18.7665308078 315.150650994
|
||||
136 3.775 17.2509296613 291.411543325
|
||||
137 3.78 15.8493332971 269.522170811
|
||||
138 3.785 14.5528796804 249.330205101
|
||||
139 3.79 13.3534346012 230.696628411
|
||||
140 3.795 12.2435282565 213.494500686
|
||||
141 3.8 11.2162976896 197.607847495
|
||||
142 3.805 10.2654345142 182.930656184
|
||||
143 3.81 9.38513741093 169.365969178
|
||||
144 3.815 8.57006893443 156.825064535
|
||||
145 3.82 7.81531621929 145.226714879
|
||||
146 3.825 7.1163552113 134.496516825
|
||||
147 3.83 6.46901809043 124.566283826
|
||||
148 3.835 5.86946358438 115.373496111
|
||||
149 3.84 5.3141499016 106.860802062
|
||||
150 3.845 4.79981003946 98.9755659598
|
||||
151 3.85 4.32342924744 91.6694575494
|
||||
152 3.855 3.88222444642 84.8980793495
|
||||
153 3.86 3.47362542484 78.6206280516
|
||||
154 3.865 3.09525764949 72.7995867184
|
||||
155 3.87 2.74492654463 67.4004448293
|
||||
156 3.875 2.42060310675 62.3914435192
|
||||
157 3.88 2.12041073521 57.7433436194
|
||||
158 3.885 1.84261317026 53.4292143513
|
||||
159 3.89 1.58560343996 49.424240734
|
||||
160 3.895 1.34789372698 45.7055479593
|
||||
161 3.9 1.12810607442 42.2520411601
|
||||
162 3.905 0.92496385733 39.0442591487
|
||||
163 3.91 0.737283953249 36.0642408427
|
||||
164 3.915 0.563969551396 33.2954032193
|
||||
165 3.92 0.404003545437 30.7224297483
|
||||
166 3.925 0.2564424599 28.3311683573
|
||||
167 3.93 0.120410864734 26.1085380703
|
||||
168 3.935 -0.00490376337106 24.0424435434
|
||||
169 3.94 -0.120255770611 22.1216967943
|
||||
170 3.945 -0.226345680979 20.3359454863
|
||||
171 3.95 -0.323824207772 18.6756071913
|
||||
172 3.955 -0.413295950251 17.1318091041
|
||||
173 3.96 -0.495322801504 15.6963327338
|
||||
174 3.965 -0.570427091298 14.3615631388
|
||||
175 3.97 -0.639094485635 13.1204423129
|
||||
176 3.975 -0.701776662868 11.9664263642
|
||||
177 3.98 -0.75889378451 10.8934461632
|
||||
178 3.985 -0.810836777335 9.89587116294
|
||||
179 3.99 -0.857969441941 8.96847612349
|
||||
180 3.995 -0.900630401683 8.10641049364
|
||||
181 4.0 -0.939134904689 7.30517022808
|
||||
182 4.005 -0.973776490618 6.56057183534
|
||||
183 4.01 -1.00482853285 5.86872847094
|
||||
184 4.015 -1.03254566588 5.22602790624
|
||||
185 4.02 -1.05716510696 4.62911221801
|
||||
186 4.025 -1.07890788015 4.07485905752
|
||||
187 4.03 -1.09797995042 3.56036436994
|
||||
188 4.035 -1.11457327471 3.08292644583
|
||||
189 4.04 -1.12886677634 2.64003119688
|
||||
190 4.045 -1.14102724873 2.22933855711
|
||||
191 4.05 -1.1512101936 1.84866991901
|
||||
192 4.055 -1.15956059893 1.49599652185
|
||||
193 4.06 -1.16621366096 1.16942871644
|
||||
194 4.065 -1.17129545464 0.867206036674
|
||||
195 4.07 -1.17492355624 0.587688014256
|
||||
196 4.075 -1.17720762184 0.329345678162
|
||||
197 4.08 -1.17824992491 0.0907536851962
|
||||
198 4.085 -1.17814585595 -0.129416967536
|
||||
199 4.09 -1.17698438715 -0.332405693416
|
||||
200 4.095 -1.17484850446 -0.519368571864
|
||||
201 4.1 -1.1718156096 -0.691384146782
|
||||
202 4.105 -1.16795789413 -0.84945880294
|
||||
203 4.11 -1.16334268761 -0.994531752529
|
||||
204 4.115 -1.15803278177 -1.12747966154
|
||||
205 4.12 -1.15208673236 -1.24912094323
|
||||
206 4.125 -1.14555914033 -1.36021974383
|
||||
207 4.13 -1.1385009138 -1.46148964359
|
||||
208 4.135 -1.1309595122 -1.55359709446
|
||||
209 4.14 -1.1229791738 -1.63716461409
|
||||
210 4.145 -1.11460112791 -1.71277375416
|
||||
211 4.15 -1.10586379267 -1.78096785987
|
||||
212 4.155 -1.09680295968 -1.84225463583
|
||||
213 4.16 -1.08745196606 -1.89710853265
|
||||
214 4.165 -1.07784185518 -1.94597296735
|
||||
215 4.17 -1.06800152657 -1.98926238963
|
||||
216 4.175 -1.05795787589 -2.02736420527
|
||||
217 4.18 -1.04773592563 -2.06064056692
|
||||
218 4.185 -1.03735894714 -2.0894300419
|
||||
219 4.19 -1.02684857465 -2.11404916577
|
||||
220 4.195 -1.01622491175 -2.13479388991
|
||||
221 4.2 -1.0055066309 -2.15194093062
|
||||
222 4.205 -0.994711066419 -2.16574902671
|
||||
223 4.21 -0.983854301441 -2.17646011217
|
||||
224 4.215 -0.972951249128 -2.18430040971
|
||||
225 4.22 -0.962015728675 -2.18948145101
|
||||
226 4.225 -0.951060536345 -2.19220102845
|
||||
227 4.23 -0.940097511927 -2.19264408348
|
||||
228 4.235 -0.92913760089 -2.19098353577
|
||||
229 4.24 -0.918190912536 -2.18738105733
|
||||
230 4.245 -0.907266774409 -2.18198779544
|
||||
231 4.25 -0.896373783212 -2.17494504784
|
||||
232 4.255 -0.885519852462 -2.16638489351
|
||||
233 4.26 -0.87471225709 -2.15643078212
|
||||
234 4.265 -0.863957675198 -2.14519808475
|
||||
235 4.27 -0.853262227147 -2.13279460887
|
||||
236 4.275 -0.842631512163 -2.11932107965
|
||||
237 4.28 -0.832070642606 -2.1048715901
|
||||
238 4.285 -0.82158427607 -2.08953402203
|
||||
239 4.29 -0.81117664544 -2.07339043986
|
||||
240 4.295 -0.800851587053 -2.056517459
|
||||
241 4.3 -0.790612567064 -2.0389865906
|
||||
242 4.305 -0.780462706161 -2.02086456422
|
||||
243 4.31 -0.770404802702 -2.00221362974
|
||||
244 4.315 -0.760441354404 -1.98309184017
|
||||
245 4.32 -0.750574578653 -1.96355331629
|
||||
246 4.325 -0.740806431546 -1.94364849462
|
||||
247 4.33 -0.731138625717 -1.92342435953
|
||||
248 4.335 -0.721572647055 -1.90292466077
|
||||
249 4.34 -0.712109770359 -1.8821901172
|
||||
250 4.345 -0.702751074011 -1.86125860773
|
||||
251 4.35 -0.693497453724 -1.84016535019
|
||||
252 4.355 -0.684349635419 -1.81894306902
|
||||
253 4.36 -0.675308187304 -1.79762215246
|
||||
254 4.365 -0.666373531174 -1.77623079981
|
||||
255 4.37 -0.657545953012 -1.75479515963
|
||||
256 4.375 -0.648825612912 -1.73333945922
|
||||
257 4.38 -0.640212554381 -1.71188612608
|
||||
258 4.385 -0.631706713048 -1.6904559018
|
||||
259 4.39 -0.623307924828 -1.66906794891
|
||||
260 4.395 -0.615015933557 -1.64773995108
|
||||
261 4.4 -0.606830398156 -1.6264882071
|
||||
262 4.405 -0.598750899326 -1.60532771911
|
||||
263 4.41 -0.590776945828 -1.58427227531
|
||||
264 4.415 -0.582907980353 -1.5633345276
|
||||
265 4.42 -0.575143385022 -1.54252606445
|
||||
266 4.425 -0.567482486527 -1.52185747923
|
||||
267 4.43 -0.559924560948 -1.5013384344
|
||||
268 4.435 -0.552468838251 -1.48097772171
|
||||
269 4.44 -0.545114506505 -1.46078331869
|
||||
270 4.445 -0.537860715815 -1.44076244171
|
||||
271 4.45 -0.530706582 -1.42092159576
|
||||
272 4.455 -0.523651190037 -1.40126662118
|
||||
273 4.46 -0.516693597271 -1.38180273752
|
||||
274 4.465 -0.509832836414 -1.36253458471
|
||||
275 4.47 -0.503067918346 -1.34346626168
|
||||
276 4.475 -0.496397834731 -1.32460136271
|
||||
277 4.48 -0.489821560449 -1.30594301139
|
||||
278 4.485 -0.483338055873 -1.28749389264
|
||||
279 4.49 -0.476946268986 -1.26925628268
|
||||
280 4.495 -0.470645137352 -1.2512320772
|
||||
281 4.5 -0.464433589953 -1.23342281778
|
||||
282 4.505 -0.458310548894 -1.21582971671
|
||||
283 4.51 -0.452274930995 -1.19845368022
|
||||
284 4.515 -0.446325649266 -1.18129533036
|
||||
285 4.52 -0.44046161427 -1.16435502548
|
||||
286 4.525 -0.4346817354 -1.14763287946
|
||||
287 4.53 -0.428984922053 -1.13112877974
|
||||
288 4.535 -0.423370084719 -1.11484240423
|
||||
289 4.54 -0.417836135987 -1.09877323723
|
||||
290 4.545 -0.41238199148 -1.08292058423
|
||||
291 4.55 -0.407006570712 -1.06728358594
|
||||
292 4.555 -0.401708797874 -1.05186123133
|
||||
293 4.56 -0.396487602569 -1.03665236991
|
||||
294 4.565 -0.391341920477 -1.02165572322
|
||||
295 4.57 -0.386270693966 -1.00686989558
|
||||
296 4.575 -0.381272872655 -0.992293384203
|
||||
297 4.58 -0.376347413926 -0.977924588641
|
||||
298 4.585 -0.371493283387 -0.963761819613
|
||||
299 4.59 -0.366709455298 -0.949803307297
|
||||
300 4.595 -0.361994912953 -0.936047209078
|
||||
301 4.6 -0.357348649027 -0.922491616798
|
||||
302 4.605 -0.352769665884 -0.909134563531
|
||||
303 4.61 -0.348256975857 -0.895974029926
|
||||
304 4.615 -0.343809601493 -0.883007950126
|
||||
305 4.62 -0.339426575775 -0.870234217299
|
||||
306 4.625 -0.335106942311 -0.857650688807
|
||||
307 4.63 -0.330849755501 -0.845255191024
|
||||
308 4.635 -0.326654080682 -0.833045523832
|
||||
309 4.64 -0.322518994248 -0.821019464813
|
||||
310 4.645 -0.318443583754 -0.809174773153
|
||||
311 4.65 -0.314426947996 -0.797509193282
|
||||
312 4.655 -0.310468197079 -0.786020458251
|
||||
313 4.66 -0.306566452464 -0.774706292883
|
||||
314 4.665 -0.302720847002 -0.763564416693
|
||||
315 4.67 -0.298930524954 -0.752592546601
|
||||
316 4.675 -0.295194641998 -0.741788399447
|
||||
317 4.68 -0.291512365223 -0.731149694325
|
||||
318 4.685 -0.287882873112 -0.720674154735
|
||||
319 4.69 -0.284305355517 -0.710359510583
|
||||
320 4.695 -0.280779013618 -0.700203500014
|
||||
321 4.7 -0.277303059881 -0.690203871119
|
||||
322 4.705 -0.273876718005 -0.680358383489
|
||||
323 4.71 -0.270499222857 -0.670664809654
|
||||
324 4.715 -0.267169820408 -0.6611209364
|
||||
325 4.72 -0.263887767656 -0.651724565975
|
||||
326 4.725 -0.260652332547 -0.64247351719
|
||||
327 4.73 -0.257462793889 -0.633365626422
|
||||
328 4.735 -0.254318441262 -0.624398748527
|
||||
329 4.74 -0.251218574926 -0.615570757662
|
||||
330 4.745 -0.248162505718 -0.606879548039
|
||||
331 4.75 -0.245149554953 -0.598323034585
|
||||
332 4.755 -0.242179054319 -0.58989915355
|
||||
333 4.76 -0.239250345768 -0.581605863034
|
||||
334 4.765 -0.236362781405 -0.573441143467
|
||||
335 4.77 -0.233515723378 -0.565402998016
|
||||
336 4.775 -0.230708543759 -0.557489452949
|
||||
337 4.78 -0.227940624433 -0.549698557946
|
||||
338 4.785 -0.225211356975 -0.542028386363
|
||||
339 4.79 -0.222520142536 -0.534477035451
|
||||
340 4.795 -0.219866391719 -0.527042626532
|
||||
341 4.8 -0.21724952446 -0.519723305146
|
||||
342 4.805 -0.214668969906 -0.512517241154
|
||||
343 4.81 -0.212124166297 -0.505422628808
|
||||
344 4.815 -0.209614560836 -0.498437686799
|
||||
345 4.82 -0.207139609574 -0.491560658268
|
||||
346 4.825 -0.204698777286 -0.484789810792
|
||||
347 4.83 -0.202291537346 -0.478123436352
|
||||
348 4.835 -0.199917371608 -0.471559851267
|
||||
349 4.84 -0.197575770285 -0.465097396123
|
||||
350 4.845 -0.195266231824 -0.458734435665
|
||||
351 4.85 -0.19298826279 -0.452469358686
|
||||
352 4.855 -0.190741377745 -0.446300577889
|
||||
353 4.86 -0.188525099125 -0.440226529743
|
||||
354 4.865 -0.186338957127 -0.434245674319
|
||||
355 4.87 -0.184182489589 -0.428356495114
|
||||
356 4.875 -0.182055241873 -0.422557498867
|
||||
357 4.88 -0.179956766747 -0.416847215362
|
||||
358 4.885 -0.177886624278 -0.41122419722
|
||||
359 4.89 -0.175844381709 -0.405687019689
|
||||
360 4.895 -0.173829613352 -0.400234280415
|
||||
361 4.9 -0.171841900476 -0.394864599219
|
||||
362 4.905 -0.169880831195 -0.389576617857
|
||||
363 4.91 -0.16794600036 -0.384368999782
|
||||
364 4.915 -0.166037009451 -0.379240429897
|
||||
365 4.92 -0.164153466471 -0.374189614305
|
||||
366 4.925 -0.16229498584 -0.369215280054
|
||||
367 4.93 -0.16046118829 -0.364316174883
|
||||
368 4.935 -0.158651700764 -0.359491066961
|
||||
369 4.94 -0.156866156312 -0.354738744625
|
||||
370 4.945 -0.155104193995 -0.350058016116
|
||||
371 4.95 -0.153365458783 -0.345447709317
|
||||
372 4.955 -0.151649601455 -0.340906671484
|
||||
373 4.96 -0.14995627851 -0.336433768983
|
||||
374 4.965 -0.148285152065 -0.33202788702
|
||||
375 4.97 -0.146635889767 -0.327687929376
|
||||
376 4.975 -0.145008164695 -0.323412818142
|
||||
377 4.98 -0.143401655276 -0.319201493452
|
||||
378 4.985 -0.141816045188 -0.315052913217
|
||||
379 4.99 -0.140251023278 -0.310966052862
|
||||
380 4.995 -0.138706283472 -0.306939905064
|
||||
381 5.0 -0.137181524691 -0.30297347949
|
||||
382 5.005 -0.135676450764 -0.299065802536
|
||||
383 5.01 -0.134190770348 -0.295215917071
|
||||
384 5.015 -0.132724196843 -0.291422882179
|
||||
385 5.02 -0.131276448317 -0.287685772906
|
||||
386 5.025 -0.129847247421 -0.284003680008
|
||||
387 5.03 -0.128436321314 -0.280375709698
|
||||
388 5.035 -0.127043401585 -0.276800983406
|
||||
389 5.04 -0.12566822418 -0.273278637523
|
||||
390 5.045 -0.124310529325 -0.269807823169
|
||||
391 5.05 -0.122970061454 -0.266387705946
|
||||
392 5.055 -0.121646569138 -0.263017465704
|
||||
393 5.06 -0.120339805013 -0.259696296304
|
||||
394 5.065 -0.119049525711 -0.256423405389
|
||||
395 5.07 -0.117775491793 -0.253198014152
|
||||
396 5.075 -0.11651746768 -0.25001935711
|
||||
397 5.08 -0.115275221587 -0.246886681885
|
||||
398 5.085 -0.114048525458 -0.243799248974
|
||||
399 5.09 -0.112837154905 -0.240756331544
|
||||
400 5.095 -0.111640889142 -0.237757215204
|
||||
401 5.1 -0.110459510922 -0.234801197803
|
||||
402 5.105 -0.109292806483 -0.231887589219
|
||||
403 5.11 -0.10814056548 -0.229015711147
|
||||
404 5.115 -0.107002580932 -0.226184896906
|
||||
405 5.12 -0.105878649164 -0.223394491231
|
||||
406 5.125 -0.104768569746 -0.220643850079
|
||||
407 5.13 -0.103672145444 -0.217932340436
|
||||
408 5.135 -0.10258918216 -0.215259340122
|
||||
409 5.14 -0.101519488881 -0.212624237608
|
||||
410 5.145 -0.100462877624 -0.210026431825
|
||||
411 5.15 -0.0994191633865 -0.207465331988
|
||||
412 5.155 -0.0983881640955 -0.204940357408
|
||||
413 5.16 -0.0973697005554 -0.202450937324
|
||||
414 5.165 -0.0963635964003 -0.199996510721
|
||||
415 5.17 -0.0953696780453 -0.197576526166
|
||||
416 5.175 -0.0943877746391 -0.195190441635
|
||||
417 5.18 -0.0934177180174 -0.192837724349
|
||||
418 5.185 -0.0924593426569 -0.190517850609
|
||||
419 5.19 -0.0915124856305 -0.188230305639
|
||||
420 5.195 -0.0905769865631 -0.185974583427
|
||||
421 5.2 -0.0896526875878 -0.18375018657
|
||||
422 5.205 -0.0887394333038 -0.18155662612
|
||||
423 5.21 -0.0878370707341 -0.179393421439
|
||||
424 5.215 -0.0869454492844 -0.177260100045
|
||||
425 5.22 -0.0860644207027 -0.175156197473
|
||||
426 5.225 -0.0851938390397 -0.173081257131
|
||||
427 5.23 -0.0843335606096 -0.17103483016
|
||||
428 5.235 -0.0834834439517 -0.169016475296
|
||||
429 5.24 -0.0826433497932 -0.167025758735
|
||||
430 5.245 -0.0818131410117 -0.165062254002
|
||||
431 5.25 -0.0809926825993 -0.163125541821
|
||||
432 5.255 -0.0801818416266 -0.161215209984
|
||||
433 5.26 -0.079380487208 -0.159330853228
|
||||
434 5.265 -0.078588490467 -0.157472073109
|
||||
435 5.27 -0.0778057245025 -0.155638477884
|
||||
436 5.275 -0.0770320643556 -0.15382968239
|
||||
437 5.28 -0.0762673869772 -0.152045307925
|
||||
438 5.285 -0.0755115711956 -0.150284982136
|
||||
439 5.29 -0.0747644976853 -0.148548338906
|
||||
440 5.295 -0.0740260489359 -0.146835018241
|
||||
441 5.3 -0.0732961092222 -0.145144666161
|
||||
442 5.305 -0.0725745645738 -0.143476934597
|
||||
443 5.31 -0.0718613027461 -0.14183148128
|
||||
444 5.315 -0.0711562131918 -0.140207969643
|
||||
445 5.32 -0.0704591870322 -0.138606068717
|
||||
446 5.325 -0.0697701170295 -0.137025453033
|
||||
447 5.33 -0.0690888975602 -0.135465802523
|
||||
448 5.335 -0.0684154245873 -0.133926802424
|
||||
449 5.34 -0.0677495956348 -0.132408143187
|
||||
450 5.345 -0.0670913097616 -0.130909520379
|
||||
451 5.35 -0.0664404675362 -0.129430634599
|
||||
452 5.355 -0.0657969710116 -0.127971191381
|
||||
453 5.36 -0.0651607237011 -0.126530901116
|
||||
454 5.365 -0.0645316305539 -0.125109478958
|
||||
455 5.37 -0.0639095979318 -0.123706644743
|
||||
456 5.375 -0.0632945335861 -0.122322122907
|
||||
457 5.38 -0.0626863466341 -0.120955642402
|
||||
458 5.385 -0.0620849475378 -0.119606936622
|
||||
459 5.39 -0.0614902480807 -0.118275743316
|
||||
460 5.395 -0.0609021613473 -0.11696180452
|
||||
461 5.4 -0.0603206017011 -0.115664866475
|
||||
462 5.405 -0.0597454847642 -0.114384679556
|
||||
463 5.41 -0.0591767273965 -0.113120998201
|
||||
464 5.415 -0.0586142476758 -0.111873580833
|
||||
465 5.42 -0.0580579648779 -0.110642189799
|
||||
466 5.425 -0.0575077994571 -0.109426591294
|
||||
467 5.43 -0.0569636730276 -0.108226555298
|
||||
468 5.435 -0.056425508344 -0.107041855505
|
||||
469 5.44 -0.0558932292835 -0.105872269263
|
||||
470 5.445 -0.0553667608274 -0.104717577509
|
||||
471 5.45 -0.0548460290437 -0.103577564704
|
||||
472 5.455 -0.0543309610691 -0.102452018771
|
||||
473 5.46 -0.0538214850925 -0.101340731041
|
||||
474 5.465 -0.0533175303375 -0.100243496185
|
||||
475 5.47 -0.0528190270461 -0.0991601121616
|
||||
476 5.475 -0.0523259064626 -0.0980903801592
|
||||
477 5.48 -0.0518381008174 -0.0970341045378
|
||||
478 5.485 -0.051355543311 -0.0959910927755
|
||||
479 5.49 -0.0508781680991 -0.0949611554144
|
||||
480 5.495 -0.0504059102771 -0.093944106007
|
||||
481 5.5 -0.0499387058651 -0.0929397610647
|
||||
482 5.505 -0.0494764917935 -0.0919479400065
|
||||
483 5.51 -0.0490192058883 -0.0909684651086
|
||||
484 5.515 -0.0485667868571 -0.0900011614554
|
||||
485 5.52 -0.0481191742754 -0.089045856891
|
||||
486 5.525 -0.0476763085723 -0.0881023819721
|
||||
487 5.53 -0.0472381310177 -0.0871705699209
|
||||
488 5.535 -0.0468045837087 -0.0862502565794
|
||||
489 5.54 -0.0463756095568 -0.0853412803652
|
||||
490 5.545 -0.0459511522751 -0.0844434822262
|
||||
491 5.55 -0.0455311563655 -0.0835567055986
|
||||
492 5.555 -0.0451155671069 -0.0826807963635
|
||||
493 5.56 -0.0447043305426 -0.0818156028054
|
||||
494 5.565 -0.0442973934684 -0.0809609755715
|
||||
495 5.57 -0.0438947034215 -0.0801167676313
|
||||
496 5.575 -0.043496208668 -0.0792828342371
|
||||
497 5.58 -0.0431018581925 -0.0784590328851
|
||||
498 5.585 -0.0427116016864 -0.0776452232778
|
||||
499 5.59 -0.0423253895371 -0.0768412672861
|
||||
500 5.595 -0.0419431728176 -0.0760470289129
|
||||
501 5.6 -0.0415649032753 -0.075262374257
|
||||
502 5.605 -0.041190533322 -0.0744871714779
|
||||
503 5.61 -0.0408200160238 -0.0737212907608
|
||||
504 5.615 -0.0404533050908 -0.0729646042826
|
||||
505 5.62 -0.0400903548671 -0.0722169861784
|
||||
506 5.625 -0.0397311203217 -0.0714783125087
|
||||
507 5.63 -0.0393755570382 -0.0707484612271
|
||||
508 5.635 -0.0390236212059 -0.0700273121483
|
||||
509 5.64 -0.0386752696104 -0.0693147469176
|
||||
510 5.645 -0.0383304596246 -0.0686106489795
|
||||
511 5.65 -0.0379891491998 -0.0679149035485
|
||||
512 5.655 -0.0376512968568 -0.0672273975789
|
||||
513 5.66 -0.0373168616773 -0.0665480197363
|
||||
514 5.665 -0.0369858032954 -0.065876660369
|
||||
515 5.67 -0.0366580818895 -0.0652132114801
|
||||
516 5.675 -0.0363336581739 -0.0645575667
|
||||
517 5.68 -0.0360124933904 -0.0639096212595
|
||||
518 5.685 -0.0356945493011 -0.0632692719635
|
||||
519 5.69 -0.03537978818 -0.0626364171647
|
||||
520 5.695 -0.0350681728056 -0.0620109567384
|
||||
521 5.7 -0.0347596664531 -0.061392792057
|
||||
522 5.705 -0.0344542328874 -0.0607818259659
|
||||
523 5.71 -0.0341518363554 -0.060177962759
|
||||
524 5.715 -0.0338524415789 -0.059581108155
|
||||
525 5.72 -0.0335560137477 -0.0589911692739
|
||||
526 5.725 -0.0332625185126 -0.0584080546145
|
||||
527 5.73 -0.0329719219782 -0.0578316740315
|
||||
528 5.735 -0.0326841906969 -0.0572619387135
|
||||
529 5.74 -0.0323992916615 -0.0566987611612
|
||||
530 5.745 -0.0321171922994 -0.0561420551663
|
||||
531 5.75 -0.0318378604656 -0.0555917357902
|
||||
532 5.755 -0.0315612644367 -0.0550477193436
|
||||
533 5.76 -0.0312873729048 -0.0545099233662
|
||||
534 5.765 -0.0310161549711 -0.0539782666069
|
||||
535 5.77 -0.0307475801402 -0.0534526690041
|
||||
536 5.775 -0.030481618314 -0.0529330516667
|
||||
537 5.78 -0.030218239786 -0.0524193368549
|
||||
538 5.785 -0.0299574152356 -0.0519114479623
|
||||
539 5.79 -0.0296991157224 -0.051409309497
|
||||
540 5.795 -0.0294433126807 -0.050912847064
|
||||
541 5.8 -0.029189977914 -0.0504219873478
|
||||
542 5.805 -0.0289390835898 -0.049936658095
|
||||
543 5.81 -0.0286906022343 -0.0494567880971
|
||||
544 5.815 -0.0284445067271 -0.0489823071741
|
||||
545 5.82 -0.0282007702961 -0.0485131461582
|
||||
546 5.825 -0.0279593665127 -0.0480492368772
|
||||
547 5.83 -0.0277202692865 -0.0475905121394
|
||||
548 5.835 -0.0274834528608 -0.0471369057172
|
||||
549 5.84 -0.0272488918076 -0.0466883523327
|
||||
550 5.845 -0.027016561023 -0.0462447876419
|
||||
551 5.85 -0.0267864357225 -0.0458061482206
|
||||
552 5.855 -0.0265584914363 -0.0453723715492
|
||||
553 5.86 -0.0263327040052 -0.0449433959991
|
||||
554 5.865 -0.0261090495757 -0.0445191608184
|
||||
555 5.87 -0.0258875045962 -0.0440996061179
|
||||
556 5.875 -0.0256680458122 -0.043684672858
|
||||
557 5.88 -0.0254506502623 -0.043274302835
|
||||
558 5.885 -0.0252352952741 -0.0428684386684
|
||||
559 5.89 -0.0250219584602 -0.0424670237876
|
||||
560 5.895 -0.0248106177138 -0.0420700024197
|
||||
561 5.9 -0.0246012512052 -0.0416773195766
|
||||
562 5.905 -0.0243938373776 -0.0412889210434
|
||||
563 5.91 -0.0241883549434 -0.0409047533657
|
||||
564 5.915 -0.0239847828804 -0.0405247638384
|
||||
565 5.92 -0.023783100428 -0.0401489004937
|
||||
566 5.925 -0.0235832870839 -0.0397771120898
|
||||
567 5.93 -0.0233853225998 -0.0394093480998
|
||||
568 5.935 -0.0231891869786 -0.0390455587005
|
||||
569 5.94 -0.0229948604704 -0.0386856947618
|
||||
570 5.945 -0.0228023235693 -0.0383297078356
|
||||
571 5.95 -0.02261155701 -0.0379775501459
|
||||
572 5.955 -0.0224225417644 -0.0376291745779
|
||||
573 5.96 -0.0222352590382 -0.0372845346683
|
||||
574 5.965 -0.022049690268 -0.0369435845953
|
||||
575 5.97 -0.0218658171179 -0.0366062791685
|
||||
576 5.975 -0.0216836214762 -0.0362725738196
|
||||
577 5.98 -0.0215030854528 -0.0359424245927
|
||||
578 5.985 -0.0213241913757 -0.0356157881351
|
||||
579 5.99 -0.0211469217882 -0.0352926216881
|
||||
580 5.995 -0.0209712594458 -0.0349728830781
|
||||
581 6.0 -0.0207971873137 -0.0346565307074
|
||||
582 6.005 -0.0206246885634 -0.034343523546
|
||||
583 6.01 -0.0204537465704 -0.0340338211226
|
||||
584 6.015 -0.0202843449109 -0.0337273835164
|
||||
585 6.02 -0.0201164673595 -0.0334241713486
|
||||
586 6.025 -0.0199500978864 -0.0331241457746
|
||||
587 6.03 -0.0197852206547 -0.0328272684755
|
||||
588 6.035 -0.0196218200176 -0.0325335016508
|
||||
589 6.04 -0.0194598805162 -0.0322428080099
|
||||
590 6.045 -0.0192993868768 -0.0319551507653
|
||||
591 6.05 -0.0191403240084 -0.0316704936245
|
||||
592 6.055 -0.0189826770001 -0.0313888007827
|
||||
593 6.06 -0.018826431119 -0.0311100369157
|
||||
594 6.065 -0.0186715718074 -0.0308341671728
|
||||
595 6.07 -0.018518084681 -0.0305611571696
|
||||
596 6.075 -0.0183659555261 -0.0302909729809
|
||||
597 6.08 -0.0182151702974 -0.0300235811346
|
||||
598 6.085 -0.0180657151159 -0.0297589486041
|
||||
599 6.09 -0.0179175762668 -0.0294970428023
|
||||
600 6.095 -0.0177707401969 -0.0292378315752
|
||||
601 6.1 -0.017625193513 -0.028981283195
|
||||
602 6.105 -0.0174809229791 -0.0287273663543
|
||||
603 6.11 -0.017337915515 -0.0284760501597
|
||||
604 6.115 -0.0171961581939 -0.0282273041259
|
||||
605 6.12 -0.0170556382404 -0.0279810981694
|
||||
606 6.125 -0.0169163430283 -0.0277374026031
|
||||
607 6.13 -0.0167782600792 -0.0274961881301
|
||||
608 6.135 -0.01664137706 -0.0272574258382
|
||||
609 6.14 -0.0165056817814 -0.0270210871943
|
||||
610 6.145 -0.0163711621956 -0.0267871440387
|
||||
611 6.15 -0.0162378063949 -0.0265555685802
|
||||
612 6.155 -0.0161056026094 -0.0263263333899
|
||||
613 6.16 -0.0159745392057 -0.0260994113969
|
||||
614 6.165 -0.0158446046847 -0.0258747758823
|
||||
615 6.17 -0.01571578768 -0.0256524004746
|
||||
616 6.175 -0.0155880769565 -0.0254322591449
|
||||
617 6.18 -0.015461461408 -0.0252143262011
|
||||
618 6.185 -0.0153359300561 -0.024998576284
|
||||
619 6.19 -0.0152114720485 -0.0247849843619
|
||||
620 6.195 -0.015088076657 -0.0245735257263
|
||||
621 6.2 -0.0149657332764 -0.024364175987
|
||||
622 6.205 -0.0148444314225 -0.0241569110676
|
||||
623 6.21 -0.0147241607307 -0.0239517072012
|
||||
624 6.215 -0.0146049109545 -0.0237485409258
|
||||
625 6.22 -0.014486671964 -0.0235473890799
|
||||
626 6.225 -0.0143694337444 -0.0233482287986
|
||||
627 6.23 -0.0142531863944 -0.0231510375089
|
||||
628 6.235 -0.0141379201248 -0.0229557929258
|
||||
629 6.24 -0.0140236252573 -0.0227624730484
|
||||
630 6.245 -0.0139102922227 -0.0225710561554
|
||||
631 6.25 -0.0137979115599 -0.0223815208018
|
||||
632 6.255 -0.0136864739141 -0.0221938458144
|
||||
633 6.26 -0.013575970036 -0.0220080102883
|
||||
634 6.265 -0.0134663907799 -0.021823993583
|
||||
635 6.27 -0.0133577271028 -0.0216417753188
|
||||
636 6.275 -0.0132499700628 -0.0214613353731
|
||||
637 6.28 -0.0131431108183 -0.0212826538767
|
||||
638 6.285 -0.013037140626 -0.0211057112104
|
||||
639 6.29 -0.0129320508404 -0.0209304880015
|
||||
640 6.295 -0.0128278329122 -0.0207569651202
|
||||
641 6.3 -0.0127244783869 -0.0205851236763
|
||||
642 6.305 -0.0126219789041 -0.020414945016
|
||||
643 6.31 -0.0125203261961 -0.0202464107184
|
||||
644 6.315 -0.0124195120866 -0.0200795025926
|
||||
645 6.32 -0.0123195284899 -0.0199142026739
|
||||
646 6.325 -0.0122203674091 -0.0197504932215
|
||||
647 6.33 -0.0121220209361 -0.0195883567147
|
||||
648 6.335 -0.0120244812493 -0.0194277758502
|
||||
649 6.34 -0.0119277406133 -0.0192687335389
|
||||
650 6.345 -0.0118317913778 -0.0191112129035
|
||||
651 6.35 -0.011736625976 -0.0189551972747
|
||||
652 6.355 -0.0116422369241 -0.0188006701892
|
||||
653 6.36 -0.0115486168203 -0.0186476153863
|
||||
654 6.365 -0.0114557583432 -0.0184960168053
|
||||
655 6.37 -0.0113636542516 -0.018345858583
|
||||
656 6.375 -0.0112722973829 -0.0181971250506
|
||||
657 6.38 -0.0111816806525 -0.0180498007315
|
||||
658 6.385 -0.0110917970524 -0.0179038703382
|
||||
659 6.39 -0.011002639651 -0.01775931877
|
||||
660 6.395 -0.0109142015915 -0.0176161311107
|
||||
661 6.4 -0.0108264760913 -0.0174742926254
|
||||
662 6.405 -0.0107394564409 -0.017333788759
|
||||
663 6.41 -0.0106531360033 -0.0171946051328
|
||||
664 6.415 -0.0105675082129 -0.0170567275427
|
||||
665 6.42 -0.0104825665746 -0.016920141957
|
||||
666 6.425 -0.0103983046631 -0.0167848345133
|
||||
667 6.43 -0.010314716122 -0.0166507915172
|
||||
668 6.435 -0.0102317946631 -0.0165179994391
|
||||
669 6.44 -0.0101495340651 -0.016386444913
|
||||
670 6.445 -0.0100679281734 -0.0162561147332
|
||||
671 6.45 -0.00998697089892 -0.0161269958531
|
||||
672 6.455 -0.0099066562175 -0.0159990753826
|
||||
673 6.46 -0.00982697816897 -0.0158723405861
|
||||
674 6.465 -0.0097479308565 -0.0157467788803
|
||||
675 6.47 -0.00966950844575 -0.0156223778326
|
||||
676 6.475 -0.00959170516422 -0.0154991251586
|
||||
677 6.48 -0.00951451530045 -0.0153770087205
|
||||
678 6.485 -0.00943793320329 -0.0152560165249
|
||||
679 6.49 -0.00936195328122 -0.0151361367211
|
||||
680 6.495 -0.00928657000161 -0.0150173575989
|
||||
681 6.5 -0.00921177789005 -0.0148996675874
|
||||
682 6.505 -0.00913757152962 -0.0147830552523
|
||||
683 6.51 -0.00906394556024 -0.0146675092947
|
||||
684 6.515 -0.00899089467799 -0.0145530185491
|
||||
685 6.52 -0.00891841363446 -0.0144395719819
|
||||
686 6.525 -0.00884649723606 -0.0143271586891
|
||||
687 6.53 -0.00877514034341 -0.0142157678952
|
||||
688 6.535 -0.0087043378707 -0.0141053889514
|
||||
689 6.54 -0.00863408478503 -0.0139960113337
|
||||
690 6.545 -0.00856437610582 -0.0138876246413
|
||||
691 6.55 -0.00849520690421 -0.0137802185952
|
||||
692 6.555 -0.0084265723024 -0.0136737830367
|
||||
693 6.56 -0.0083584674731 -0.0135683079253
|
||||
694 6.565 -0.00829088763895 -0.0134637833379
|
||||
695 6.57 -0.00822382807187 -0.0133601994666
|
||||
696 6.575 -0.00815728409258 -0.0132575466177
|
||||
697 6.58 -0.00809125106997 -0.01315581521
|
||||
698 6.585 -0.00802572442054 -0.0130549957733
|
||||
699 6.59 -0.00796069960789 -0.0129550789471
|
||||
700 6.595 -0.00789617214214 -0.0128560554792
|
||||
701 6.6 -0.00783213757941 -0.0127579162242
|
||||
702 6.605 -0.00776859152128 -0.0126606521422
|
||||
703 6.61 -0.00770552961427 -0.0125642542974
|
||||
704 6.615 -0.00764294754931 -0.0124687138569
|
||||
705 6.62 -0.00758084106125 -0.0123740220889
|
||||
706 6.625 -0.00751920592835 -0.0122801703624
|
||||
707 6.63 -0.00745803797178 -0.0121871501447
|
||||
708 6.635 -0.00739733305512 -0.0120949530012
|
||||
709 6.64 -0.00733708708388 -0.0120035705934
|
||||
710 6.645 -0.00727729600504 -0.0119129946781
|
||||
711 6.65 -0.00721795580654 -0.0118232171061
|
||||
712 6.655 -0.00715906251684 -0.0117342298209
|
||||
713 6.66 -0.00710061220446 -0.0116460248577
|
||||
714 6.665 -0.00704260097752 -0.011558594342
|
||||
715 6.67 -0.00698502498328 -0.0114719304888
|
||||
716 6.675 -0.0069278804077 -0.011386025601
|
||||
717 6.68 -0.00687116347501 -0.0113008720688
|
||||
718 6.685 -0.00681487044729 -0.0112164623683
|
||||
719 6.69 -0.00675899762401 -0.0111327890605
|
||||
720 6.695 -0.00670354134163 -0.0110498447902
|
||||
721 6.7 -0.00664849797317 -0.010967622285
|
||||
722 6.705 -0.00659386392783 -0.0108861143542
|
||||
723 6.71 -0.00653963565053 -0.0108053138879
|
||||
724 6.715 -0.00648580962156 -0.0107252138558
|
||||
725 6.72 -0.00643238235617 -0.0106458073064
|
||||
726 6.725 -0.00637935040415 -0.0105670873659
|
||||
727 6.73 -0.00632671034949 -0.0104890472373
|
||||
728 6.735 -0.00627445880997 -0.0104116801994
|
||||
729 6.74 -0.00622259243676 -0.0103349796058
|
||||
730 6.745 -0.00617110791413 -0.0102589388842
|
||||
731 6.75 -0.00612000195897 -0.0101835515351
|
||||
732 6.755 -0.00606927132054 -0.0101088111315
|
||||
733 6.76 -0.00601891278001 -0.0100347113173
|
||||
734 6.765 -0.00596892315019 -0.00996124580682
|
||||
735 6.77 -0.00591929927513 -0.00988840838405
|
||||
736 6.775 -0.00587003802979 -0.00981619290146
|
||||
737 6.78 -0.00582113631969 -0.00974459327937
|
||||
738 6.785 -0.00577259108059 -0.00967360350506
|
||||
739 6.79 -0.00572439927814 -0.00960321763197
|
||||
740 6.795 -0.00567655790757 -0.00953342977884
|
||||
741 6.8 -0.00562906399335 -0.009464234129
|
||||
742 6.805 -0.00558191458887 -0.00939562492948
|
||||
743 6.81 -0.00553510677612 -0.00932759649031
|
||||
744 6.815 -0.00548863766541 -0.00926014318374
|
||||
745 6.82 -0.00544250439501 -0.00919325944343
|
||||
746 6.825 -0.00539670413088 -0.00912693976378
|
||||
747 6.83 -0.00535123406635 -0.00906117869914
|
||||
748 6.835 -0.00530609142185 -0.0089959708631
|
||||
749 6.84 -0.00526127344456 -0.00893131092779
|
||||
750 6.845 -0.00521677740819 -0.00886719362314
|
||||
751 6.85 -0.00517260061263 -0.0088036137362
|
||||
752 6.855 -0.00512874038373 -0.00874056611047
|
||||
753 6.86 -0.00508519407293 -0.00867804564517
|
||||
754 6.865 -0.00504195905709 -0.00861604729463
|
||||
755 6.87 -0.00499903273812 -0.00855456606758
|
||||
756 6.875 -0.00495641254277 -0.00849359702652
|
||||
757 6.88 -0.00491409592235 -0.00843313528707
|
||||
758 6.885 -0.00487208035245 -0.00837317601735
|
||||
759 6.89 -0.0048303633327 -0.00831371443731
|
||||
760 6.895 -0.00478894238648 -0.00825474581818
|
||||
761 6.9 -0.00474781506071 -0.00819626548178
|
||||
762 6.905 -0.00470697892557 -0.00813826879998
|
||||
763 6.91 -0.00466643157426 -0.00808075119406
|
||||
764 6.915 -0.00462617062273 -0.00802370813416
|
||||
765 6.92 -0.00458619370948 -0.00796713513869
|
||||
766 6.925 -0.00454649849529 -0.00791102777373
|
||||
767 6.93 -0.004507082663 -0.0078553816525
|
||||
768 6.935 -0.00446794391726 -0.00780019243478
|
||||
769 6.94 -0.00442907998431 -0.00774545582638
|
||||
770 6.945 -0.00439048861173 -0.00769116757859
|
||||
771 6.95 -0.00435216756826 -0.00763732348763
|
||||
772 6.955 -0.00431411464353 -0.00758391939413
|
||||
773 6.96 -0.00427632764786 -0.00753095118263
|
||||
774 6.965 -0.00423880441202 -0.00747841478103
|
||||
775 6.97 -0.00420154278708 -0.0074263061601
|
||||
776 6.975 -0.0041645406441 -0.00737462133297
|
||||
777 6.98 -0.004127795874 -0.00732335635464
|
||||
778 6.985 -0.00409130638732 -0.0072725073215
|
||||
779 6.99 -0.00405507011399 -0.00722207037082
|
||||
780 6.995 -0.00401908500318 -0.00717204168032
|
||||
781 7.0 -0.00398334902306 -0.00712241746764
|
||||
782 7.005 -0.00394786016061 -0.00707319398991
|
||||
783 7.01 -0.00391261642144 -0.00702436754329
|
||||
784 7.015 -0.00387761582957 -0.00697593446253
|
||||
785 7.02 -0.00384285642725 -0.00692789112049
|
||||
786 7.025 -0.00380833627479 -0.00688023392772
|
||||
787 7.03 -0.00377405345032 -0.00683295933202
|
||||
788 7.035 -0.00374000604966 -0.006786063818
|
||||
789 7.04 -0.00370619218613 -0.00673954390668
|
||||
790 7.045 -0.00367260999033 -0.00669339615506
|
||||
791 7.05 -0.00363925761 -0.0066476171557
|
||||
792 7.055 -0.00360613320981 -0.00660220353629
|
||||
793 7.06 -0.00357323497123 -0.00655715195929
|
||||
794 7.065 -0.00354056109232 -0.00651245912153
|
||||
795 7.07 -0.00350810978757 -0.00646812175376
|
||||
796 7.075 -0.00347587928773 -0.00642413662034
|
||||
797 7.08 -0.00344386783965 -0.00638050051877
|
||||
798 7.085 -0.00341207370611 -0.0063372102794
|
||||
799 7.09 -0.00338049516565 -0.006294262765
|
||||
800 7.095 -0.00334913051243 -0.0062516548704
|
||||
801 7.1 -0.00331797805604 -0.00620938352214
|
||||
802 7.105 -0.00328703612137 -0.00616744567807
|
||||
803 7.11 -0.00325630304843 -0.00612583832708
|
||||
804 7.115 -0.00322577719224 -0.00608455848864
|
||||
805 7.12 -0.00319545692261 -0.00604360321253
|
||||
806 7.125 -0.00316534062405 -0.00600296957848
|
||||
807 7.13 -0.00313542669558 -0.00596265469582
|
||||
808 7.135 -0.00310571355061 -0.00592265570314
|
||||
809 7.14 -0.00307619961678 -0.005882969768
|
||||
810 7.145 -0.00304688333584 -0.00584359408654
|
||||
811 7.15 -0.00301776316346 -0.00580452588324
|
||||
812 7.155 -0.00298883756913 -0.00576576241051
|
||||
813 7.16 -0.002960105036 -0.00572730094846
|
||||
814 7.165 -0.00293156406078 -0.00568913880453
|
||||
815 7.17 -0.00290321315354 -0.00565127331323
|
||||
816 7.175 -0.00287505083762 -0.0056137018358
|
||||
817 7.18 -0.00284707564951 -0.00557642175992
|
||||
818 7.185 -0.00281928613867 -0.00553943049944
|
||||
819 7.19 -0.00279168086743 -0.00550272549407
|
||||
820 7.195 -0.00276425841086 -0.00546630420907
|
||||
821 7.2 -0.00273701735665 -0.00543016413502
|
||||
822 7.205 -0.00270995630497 -0.00539430278748
|
||||
823 7.21 -0.00268307386833 -0.00535871770676
|
||||
824 7.215 -0.00265636867152 -0.00532340645761
|
||||
825 7.22 -0.00262983935139 -0.00528836662899
|
||||
826 7.225 -0.00260348455684 -0.00525359583375
|
||||
827 7.23 -0.00257730294861 -0.00521909170842
|
||||
828 7.235 -0.00255129319921 -0.00518485191292
|
||||
829 7.24 -0.00252545399279 -0.00515087413029
|
||||
830 7.245 -0.00249978402504 -0.00511715606646
|
||||
831 7.25 -0.00247428200305 -0.00508369545
|
||||
832 7.255 -0.00244894664521 -0.00505049003185
|
||||
833 7.26 -0.00242377668111 -0.0050175375851
|
||||
834 7.265 -0.00239877085142 -0.00498483590472
|
||||
835 7.27 -0.00237392790776 -0.00495238280735
|
||||
836 7.275 -0.00234924661264 -0.00492017613103
|
||||
837 7.28 -0.00232472573932 -0.004888213735
|
||||
838 7.285 -0.00230036407169 -0.00485649349945
|
||||
839 7.29 -0.00227616040422 -0.00482501332528
|
||||
840 7.295 -0.0022521135418 -0.00479377113392
|
||||
841 7.3 -0.00222822229968 -0.00476276486705
|
||||
842 7.305 -0.00220448550332 -0.00473199248642
|
||||
843 7.31 -0.00218090198837 -0.00470145197362
|
||||
844 7.315 -0.00215747060047 -0.00467114132986
|
||||
845 7.32 -0.00213419019525 -0.00464105857576
|
||||
846 7.325 -0.00211105963817 -0.00461120175114
|
||||
847 7.33 -0.00208807780443 -0.00458156891484
|
||||
848 7.335 -0.00206524357891 -0.00455215814447
|
||||
849 7.34 -0.00204255585605 -0.00452296753622
|
||||
850 7.345 -0.00202001353975 -0.00449399520468
|
||||
851 7.35 -0.00199761554332 -0.00446523928264
|
||||
852 7.355 -0.00197536078933 -0.00443669792087
|
||||
853 7.36 -0.00195324820956 -0.00440836928794
|
||||
854 7.365 -0.00193127674492 -0.00438025157005
|
||||
855 7.37 -0.00190944534533 -0.00435234297081
|
||||
856 7.375 -0.00188775296965 -0.00432464171107
|
||||
857 7.38 -0.00186619858559 -0.00429714602873
|
||||
858 7.385 -0.00184478116965 -0.00426985417856
|
||||
859 7.39 -0.00182349970697 -0.00424276443203
|
||||
860 7.395 -0.00180235319134 -0.00421587507713
|
||||
861 7.4 -0.00178134062504 -0.00418918441815
|
||||
862 7.405 -0.0017604610188 -0.0041626907756
|
||||
863 7.41 -0.0017397133917 -0.00413639248593
|
||||
864 7.415 -0.0017190967711 -0.00411028790146
|
||||
865 7.42 -0.00169861019256 -0.00408437539014
|
||||
866 7.425 -0.00167825269977 -0.00405865333542
|
||||
867 7.43 -0.00165802334445 -0.00403312013606
|
||||
868 7.435 -0.00163792118629 -0.00400777420601
|
||||
869 7.44 -0.00161794529289 -0.00398261397421
|
||||
870 7.445 -0.00159809473965 -0.00395763788446
|
||||
871 7.45 -0.00157836860971 -0.00393284439525
|
||||
872 7.455 -0.00155876599391 -0.00390823197958
|
||||
873 7.46 -0.00153928599065 -0.00388379912488
|
||||
874 7.465 -0.00151992770589 -0.00385954433278
|
||||
875 7.47 -0.00150069025303 -0.00383546611901
|
||||
876 7.475 -0.00148157275285 -0.00381156301323
|
||||
877 7.48 -0.00146257433348 -0.0037878335589
|
||||
878 7.485 -0.00144369413025 -0.00376427631313
|
||||
879 7.49 -0.00142493128571 -0.00374088984652
|
||||
880 7.495 -0.00140628494952 -0.00371767274304
|
||||
881 7.5 -0.00138775427835 -0.00369462359991
|
||||
882 7.505 -0.0013693384359 -0.00367174102741
|
||||
883 7.51 -0.00135103659275 -0.00364902364878
|
||||
884 7.515 -0.00133284792636 -0.00362647010008
|
||||
885 7.52 -0.00131477162096 -0.00360407903007
|
||||
886 7.525 -0.0012968068675 -0.00358184910005
|
||||
887 7.53 -0.0012789528636 -0.00355977898374
|
||||
888 7.535 -0.00126120881349 -0.00353786736716
|
||||
889 7.54 -0.00124357392793 -0.00351611294851
|
||||
890 7.545 -0.00122604742416 -0.00349451443802
|
||||
891 7.55 -0.00120862852584 -0.00347307055786
|
||||
892 7.555 -0.00119131646298 -0.00345178004197
|
||||
893 7.56 -0.0011741104719 -0.00343064163599
|
||||
894 7.565 -0.00115700979517 -0.0034096540971
|
||||
895 7.57 -0.00114001368154 -0.00338881619393
|
||||
896 7.575 -0.00112312138587 -0.00336812670643
|
||||
897 7.58 -0.00110633216913 -0.00334758442575
|
||||
898 7.585 -0.00108964529827 -0.00332718815413
|
||||
899 7.59 -0.00107306004622 -0.00330693670479
|
||||
900 7.595 -0.00105657569181 -0.00328682890181
|
||||
901 7.6 -0.00104019151973 -0.00326686358005
|
||||
902 7.605 -0.00102390682047 -0.00324703958498
|
||||
903 7.61 -0.00100772089024 -0.00322735577263
|
||||
904 7.615 -0.000991633030992 -0.00320781100945
|
||||
905 7.62 -0.000975642550274 -0.00318840417222
|
||||
906 7.625 -0.000959748761248 -0.00316913414793
|
||||
907 7.63 -0.000943950982612 -0.00314999983371
|
||||
908 7.635 -0.00092824853855 -0.00313100013668
|
||||
909 7.64 -0.000912640758688 -0.00311213397388
|
||||
910 7.645 -0.000897126978043 -0.00309340027216
|
||||
911 7.65 -0.000881706536971 -0.0030747979681
|
||||
912 7.655 -0.000866378781123 -0.00305632600787
|
||||
913 7.66 -0.000851143061394 -0.00303798334719
|
||||
914 7.665 -0.000835998733877 -0.00301976895117
|
||||
915 7.67 -0.000820945159817 -0.00300168179428
|
||||
916 7.675 -0.000805981705564 -0.0029837208602
|
||||
917 7.68 -0.000791107742523 -0.00296588514177
|
||||
918 7.685 -0.000776322647117 -0.00294817364088
|
||||
919 7.69 -0.000761625800734 -0.00293058536838
|
||||
920 7.695 -0.000747016589687 -0.00291311934398
|
||||
921 7.7 -0.000732494405167 -0.00289577459618
|
||||
922 7.705 -0.000718058643203 -0.00287855016219
|
||||
923 7.71 -0.000703708704613 -0.0028614450878
|
||||
924 7.715 -0.000689443994968 -0.00284445842736
|
||||
925 7.72 -0.000675263924546 -0.00282758924361
|
||||
926 7.725 -0.000661167908286 -0.0028108366077
|
||||
927 7.73 -0.000647155365757 -0.002794199599
|
||||
928 7.735 -0.000633225721105 -0.00277767730511
|
||||
929 7.74 -0.000619378403022 -0.00276126882172
|
||||
930 7.745 -0.000605612844698 -0.00274497325255
|
||||
931 7.75 -0.000591928483787 -0.00272878970927
|
||||
932 7.755 -0.000578324762364 -0.00271271731143
|
||||
933 7.76 -0.000564801126885 -0.00269675518635
|
||||
934 7.765 -0.000551357028154 -0.00268090246909
|
||||
935 7.77 -0.000537991921277 -0.00266515830234
|
||||
936 7.775 -0.00052470526563 -0.00264952183636
|
||||
937 7.78 -0.000511496524817 -0.00263399222891
|
||||
938 7.785 -0.000498365166635 -0.00261856864514
|
||||
939 7.79 -0.000485310663039 -0.00260325025757
|
||||
940 7.795 -0.0004723324901 -0.00258803624599
|
||||
941 7.8 -0.000459430127974 -0.00257292579737
|
||||
942 7.805 -0.000446603060865 -0.00255791810586
|
||||
943 7.81 -0.000433850776986 -0.00254301237261
|
||||
944 7.815 -0.000421172768528 -0.00252820780582
|
||||
945 7.82 -0.000408568531625 -0.00251350362058
|
||||
946 7.825 -0.000396037566317 -0.00249889903884
|
||||
947 7.83 -0.000383579376517 -0.00248439328937
|
||||
948 7.835 -0.000371193469977 -0.00246998560763
|
||||
949 7.84 -0.000358879358258 -0.00245567523575
|
||||
950 7.845 -0.000346636556689 -0.00244146142247
|
||||
951 7.85 -0.000334464584344 -0.00242734342306
|
||||
952 7.855 -0.000322362964 -0.00241332049923
|
||||
953 7.86 -0.000310331222112 -0.00239939191913
|
||||
954 7.865 -0.000298368888779 -0.00238555695723
|
||||
955 7.87 -0.000286475497709 -0.00237181489431
|
||||
956 7.875 -0.000274650586192 -0.00235816501734
|
||||
957 7.88 -0.00026289369507 -0.00234460661948
|
||||
958 7.885 -0.000251204368701 -0.00233113899997
|
||||
959 7.89 -0.000239582154932 -0.00231776146411
|
||||
960 7.895 -0.000228026605069 -0.00230447332318
|
||||
961 7.9 -0.000216537273846 -0.0022912738944
|
||||
962 7.905 -0.000205113719399 -0.00227816250086
|
||||
963 7.91 -0.000193755503231 -0.00226513847144
|
||||
964 7.915 -0.000182462190187 -0.00225220114081
|
||||
965 7.92 -0.000171233348425 -0.00223934984935
|
||||
966 7.925 -0.000160068549386 -0.00222658394306
|
||||
967 7.93 -0.000148967367767 -0.00221390277357
|
||||
968 7.935 -0.000137929381494 -0.00220130569803
|
||||
969 7.94 -0.000126954171692 -0.00218879207909
|
||||
970 7.945 -0.000116041322662 -0.00217636128485
|
||||
971 7.95 -0.000105190421847 -0.00216401268878
|
||||
972 7.955 -9.44010598127e-05 -0.00215174566969
|
||||
973 7.96 -8.36728302154e-05 -0.0021395596117
|
||||
974 7.965 -7.30053297786e-05 -0.00212745390412
|
||||
975 7.97 -6.23981582662e-05 -0.00211542794149
|
||||
976 7.975 -5.18509184563e-05 -0.00210348112347
|
||||
977 7.98 -4.13632161162e-05 -0.0020916128548
|
||||
978 7.985 -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
|
||||
@ -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 25.5521313672 336.473698771
|
||||
137 3.78 23.9289303577 313.111564661
|
||||
138 3.785 22.4180927206 291.503678217
|
||||
139 3.79 21.0112064166 271.508493474
|
||||
140 3.795 19.7005361332 252.996669413
|
||||
141 3.8 18.4789651059 235.849950713
|
||||
142 3.805 17.3399422592 219.960157211
|
||||
143 3.81 16.2774341511 205.228270919
|
||||
144 3.815 15.2858812611 191.563610676
|
||||
145 3.82 14.3601582029 178.88308554
|
||||
146 3.825 13.4955374911 167.110519006
|
||||
147 3.83 12.6876565243 156.176036954
|
||||
148 3.835 11.9324874825 146.015512988
|
||||
149 3.84 11.2263098661 136.570065484
|
||||
150 3.845 10.5656854316 127.785601256
|
||||
151 3.85 9.94743530166 119.612401285
|
||||
152 3.855 9.36861904981 112.004744426
|
||||
153 3.86 8.82651557999 104.920565393
|
||||
154 3.865 8.31860563683 98.3211437563
|
||||
155 3.87 7.84255579999 92.1708209642
|
||||
156 3.875 7.39620382887 86.4367427306
|
||||
157 3.88 6.97754523696 81.0886243871
|
||||
158 3.885 6.58472098661 76.0985370389
|
||||
159 3.89 6.21600620515 71.4407125773
|
||||
160 3.895 5.86979983242 67.0913657925
|
||||
161 3.9 5.54461511838 63.0285320059
|
||||
162 3.905 5.23907089671 59.2319187891
|
||||
163 3.91 4.95188356739 55.6827704829
|
||||
164 3.915 4.68185972707 52.3637443466
|
||||
165 3.92 4.42788939186 49.2587972858
|
||||
166 3.925 4.18893976204 46.353082203
|
||||
167 3.93 3.96404948281 43.6328531095
|
||||
168 3.935 3.75232335915 41.0853782151
|
||||
169 3.94 3.55292748687 38.6988602882
|
||||
170 3.945 3.36508476491 36.4623636443
|
||||
171 3.95 3.18807075749 34.3657471793
|
||||
172 3.955 3.021209877 32.3996029206
|
||||
173 3.96 2.86387186138 30.5551996145
|
||||
174 3.965 2.71546852189 28.8244309147
|
||||
175 3.97 2.57545073925 27.1997677761
|
||||
176 3.975 2.44330568809 25.6742146917
|
||||
177 3.98 2.31855427126 24.2412694474
|
||||
178 3.985 2.20074874724 22.8948860937
|
||||
179 3.99 2.08947053515 21.6294408646
|
||||
180 3.995 1.98432818342 20.4397007945
|
||||
181 4.0 1.88495548901 19.3207948084
|
||||
182 4.005 1.79100975549 18.2681870794
|
||||
183 4.01 1.70217017901 17.2776524655
|
||||
184 4.015 1.61813635232 16.3452538542
|
||||
185 4.02 1.53862687753 15.467321259
|
||||
186 4.025 1.4633780794 14.6404325234
|
||||
187 4.03 1.3921428113 13.8613955037
|
||||
188 4.035 1.32468934683 13.1272316094
|
||||
189 4.04 1.26080035064 12.435160592
|
||||
190 4.045 1.20027192224 11.7825864834
|
||||
191 4.05 1.14291270762 11.1670845906
|
||||
192 4.055 1.08854307328 10.5863894642
|
||||
193 4.06 1.03699433825 10.0383837622
|
||||
194 4.065 0.988108059646 9.5210879405
|
||||
195 4.07 0.941735367837 9.03265070365
|
||||
196 4.075 0.897736347632 8.57134015767
|
||||
197 4.08 0.855979462015 8.13553560989
|
||||
198 4.085 0.816341015387 7.72371996598
|
||||
199 4.09 0.778704653425 7.33447267828
|
||||
200 4.095 0.74296089691 6.96646320305
|
||||
201 4.1 0.709006707075 6.61844492796
|
||||
202 4.105 0.676745080218 6.28924953404
|
||||
203 4.11 0.646084669489 5.97778175928
|
||||
204 4.115 0.616939431912 5.68301453361
|
||||
205 4.12 0.589228298872 5.40398445752
|
||||
206 4.125 0.562874868393 5.13978759855
|
||||
207 4.13 0.537807117698 4.88957558211
|
||||
208 4.135 0.513957134618 4.65255195486
|
||||
209 4.14 0.491260866548 4.42796880052
|
||||
210 4.145 0.469657885731 4.21512358966
|
||||
211 4.15 0.449091169745 4.01335624628
|
||||
212 4.155 0.429506896145 3.82204641559
|
||||
213 4.16 0.410854250299 3.64061091811
|
||||
214 4.165 0.393085245513 3.46850137704
|
||||
215 4.17 0.376154554607 3.30520200609
|
||||
216 4.175 0.360019352187 3.15022754657
|
||||
217 4.18 0.34463916687 3.00312134286
|
||||
218 4.185 0.329975742808 2.86345354671
|
||||
219 4.19 0.315992909894 2.730819441
|
||||
220 4.195 0.30265646206 2.60483787474
|
||||
221 4.2 0.289934043143 2.48514980144
|
||||
222 4.205 0.277795039817 2.37141691363
|
||||
223 4.21 0.26621048112 2.26332036686
|
||||
224 4.215 0.255152944156 2.160559587
|
||||
225 4.22 0.244596465565 2.06285115501
|
||||
226 4.225 0.234516458378 1.96992776403
|
||||
227 4.23 0.22488963393 1.88153724361
|
||||
228 4.235 0.215693928479 1.79744164671
|
||||
229 4.24 0.206908434252 1.71741639508
|
||||
230 4.245 0.198513334625 1.64124947915
|
||||
231 4.25 0.190489843169 1.56874070868
|
||||
232 4.255 0.182820146331 1.49970101084
|
||||
233 4.26 0.175487349508 1.43395177247
|
||||
234 4.265 0.168475426305 1.3713242237
|
||||
235 4.27 0.16176917078 1.31165886002
|
||||
236 4.275 0.155354152487 1.2548049004
|
||||
237 4.28 0.149216674142 1.20061977901
|
||||
238 4.285 0.143343731751 1.1489686684
|
||||
239 4.29 0.137722977049 1.09972403198
|
||||
240 4.295 0.13234268211 1.05276520399
|
||||
241 4.3 0.127191705983 1.00797799517
|
||||
242 4.305 0.122259463251 0.965254322417
|
||||
243 4.31 0.117535894375 0.924491860866
|
||||
244 4.315 0.113011437731 0.885593717092
|
||||
245 4.32 0.108677003225 0.848468121932
|
||||
246 4.325 0.104523947407 0.813028141752
|
||||
247 4.33 0.100544049971 0.779191406981
|
||||
248 4.335 0.0967294915884 0.746879856814
|
||||
249 4.34 0.0930728329625 0.716019499063
|
||||
250 4.345 0.0895669950612 0.686540184216
|
||||
251 4.35 0.0862052404384 0.658375392808
|
||||
252 4.355 0.08298115559 0.63146203527
|
||||
253 4.36 0.0798886342796 0.605740263498
|
||||
254 4.365 0.0769218617798 0.5811532934
|
||||
255 4.37 0.0740752999737 0.557647237752
|
||||
256 4.375 0.0713436732684 0.535170948731
|
||||
257 4.38 0.0687219552728 0.513675869532
|
||||
258 4.385 0.0662053561949 0.493115894506
|
||||
259 4.39 0.0637893109199 0.473447237321
|
||||
260 4.395 0.0614694677263 0.45462830664
|
||||
261 4.4 0.0592416776079 0.436619588871
|
||||
262 4.405 0.0571019841636 0.419383537567
|
||||
263 4.41 0.0550466140255 0.402884469071
|
||||
264 4.415 0.0530719677933 0.387088464035
|
||||
265 4.42 0.0511746114473 0.371963274467
|
||||
266 4.425 0.0493512682135 0.357478235973
|
||||
267 4.43 0.0475988108542 0.343604184887
|
||||
268 4.435 0.0459142543625 0.33031338001
|
||||
269 4.44 0.0442947490359 0.317579428671
|
||||
270 4.445 0.0427375739105 0.305377216875
|
||||
271 4.45 0.041240130534 0.293682843283
|
||||
272 4.455 0.0397999370598 0.282473556818
|
||||
273 4.46 0.0384146226445 0.271727697674
|
||||
274 4.465 0.0370819221326 0.261424641529
|
||||
275 4.47 0.035799671012 0.251544746799
|
||||
276 4.475 0.034565800626 0.242069304731
|
||||
277 4.48 0.0333783336288 0.232980492193
|
||||
278 4.485 0.0322353796696 0.224261326994
|
||||
279 4.49 0.0311351312947 0.215895625604
|
||||
280 4.495 0.0300758600554 0.207867963122
|
||||
281 4.5 0.0290559128103 0.200163635378
|
||||
282 4.505 0.0280737082121 0.192768623045
|
||||
283 4.51 0.0271277333693 0.185669557645
|
||||
284 4.515 0.0262165406731 0.178853689349
|
||||
285 4.52 0.0253387447812 0.172308856461
|
||||
286 4.525 0.0244930197498 0.166023456513
|
||||
287 4.53 0.023678096307 0.159986418851
|
||||
288 4.535 0.0228927592589 0.154187178661
|
||||
289 4.54 0.0221358450227 0.148615652333
|
||||
290 4.545 0.0214062392796 0.143262214105
|
||||
291 4.55 0.0207028747413 0.138117673905
|
||||
292 4.555 0.0200247290247 0.133173256332
|
||||
293 4.56 0.0193708226289 0.128420580717
|
||||
294 4.565 0.018740217009 0.123851642198
|
||||
295 4.57 0.0181320127424 0.119458793758
|
||||
296 4.575 0.017545347783 0.115234729179
|
||||
297 4.58 0.0169793957974 0.111172466848
|
||||
298 4.585 0.0164333645811 0.107265334394
|
||||
299 4.59 0.0159064945488 0.103506954082
|
||||
300 4.595 0.0153980572965 0.0998912289493
|
||||
301 4.6 0.0149073542304 0.0964123296321
|
||||
302 4.605 0.0144337152611 0.0930646818445
|
||||
303 4.61 0.0139764975575 0.0898429544837
|
||||
304 4.615 0.0135350843599 0.086742048322
|
||||
305 4.62 0.0131088838475 0.0837570852568
|
||||
306 4.625 0.0126973280587 0.0808833980908
|
||||
307 4.63 0.0122998718608 0.0781165208124
|
||||
308 4.635 0.0119159919677 0.0754521793521
|
||||
309 4.64 0.0115451860021 0.07288628279
|
||||
310 4.645 0.0111869716011 0.0704149149899
|
||||
311 4.65 0.010840885562 0.0680343266405
|
||||
312 4.655 0.0105064830275 0.0657409276799
|
||||
313 4.66 0.0101833367076 0.063531280086
|
||||
314 4.665 0.0098710361368 0.0614020910133
|
||||
315 4.67 0.00956918696433 0.0593502062585
|
||||
316 4.675 0.00927741027701 0.0573726040383
|
||||
317 4.68 0.00899534195191 0.0554663890638
|
||||
318 4.685 0.00872263203811 0.0536287868959
|
||||
319 4.69 0.00845894416602 0.0518571385691
|
||||
320 4.695 0.0082039549829 0.0501488954678
|
||||
321 4.7 0.00795735361347 0.0485016144454
|
||||
322 4.705 0.00771884114422 0.0469129531714
|
||||
323 4.71 0.00748813013054 0.045380665697
|
||||
324 4.715 0.00726494412547 0.0439025982277
|
||||
325 4.72 0.00704901722906 0.0424766850927
|
||||
326 4.725 0.00684009365745 0.0411009449015
|
||||
327 4.73 0.00663792733071 0.0397734768782
|
||||
328 4.735 0.00644228147858 0.0384924573653
|
||||
329 4.74 0.00625292826325 0.0372561364888
|
||||
330 4.745 0.00606964841851 0.0360628349754
|
||||
331 4.75 0.00589223090433 0.0349109411165
|
||||
332 4.755 0.00572047257643 0.0337989078704
|
||||
333 4.76 0.0055541778698 0.0327252500962
|
||||
334 4.765 0.00539315849596 0.0316885419138
|
||||
335 4.77 0.00523723315293 0.0306874141829
|
||||
336 4.775 0.00508622724762 0.0297205520964
|
||||
337 4.78 0.00493997262995 0.0287866928817
|
||||
338 4.785 0.00479830733822 0.0278846236056
|
||||
339 4.79 0.00466107535518 0.0270131790775
|
||||
340 4.795 0.00452812637438 0.0261712398457
|
||||
341 4.8 0.00439931557628 0.0253577302837
|
||||
342 4.805 0.00427450341372 0.0245716167613
|
||||
343 4.81 0.00415355540638 0.0238119058963
|
||||
344 4.815 0.00403634194372 0.0230776428841
|
||||
345 4.82 0.00392273809612 0.0223679099007
|
||||
346 4.825 0.00381262343384 0.0216818245753
|
||||
347 4.83 0.00370588185338 0.021018538531
|
||||
348 4.835 0.00360240141109 0.0203772359884
|
||||
349 4.84 0.00350207416352 0.0197571324301
|
||||
350 4.845 0.0034047960143 0.019157473324
|
||||
351 4.85 0.00331046656734 0.0185775329012
|
||||
352 4.855 0.00321898898591 0.0180166129873
|
||||
353 4.86 0.00313026985753 0.0174740418837
|
||||
354 4.865 0.00304421906424 0.0169491732974
|
||||
355 4.87 0.00296074965818 0.0164413853165
|
||||
356 4.875 0.00287977774216 0.0159500794299
|
||||
357 4.88 0.002801222355 0.0154746795881
|
||||
358 4.885 0.0027250053615 0.0150146313053
|
||||
359 4.89 0.00265105134676 0.0145694007979
|
||||
360 4.895 0.0025792875148 0.0141384741613
|
||||
361 4.9 0.00250964359108 0.0137213565802
|
||||
362 4.905 0.00244205172902 0.0133175715727
|
||||
363 4.91 0.00237644642012 0.0129266602662
|
||||
364 4.915 0.00231276440768 0.0125481807036
|
||||
365 4.92 0.00225094460389 0.0121817071786
|
||||
366 4.925 0.00219092801016 0.0118268295982
|
||||
367 4.93 0.00213265764061 0.011483152873
|
||||
368 4.935 0.00207607844856 0.011150296331
|
||||
369 4.94 0.00202113725576 0.0108278931578
|
||||
370 4.945 0.00196778268457 0.0105155898576
|
||||
371 4.95 0.00191596509257 0.0102130457388
|
||||
372 4.955 0.00186563650984 0.00991993241864
|
||||
373 4.96 0.0018167505786 0.00963593334953
|
||||
374 4.965 0.00176926249515 0.0093607433642
|
||||
375 4.97 0.0017231289541 0.00909406823946
|
||||
376 4.975 0.00167830809471 0.00883562427782
|
||||
377 4.98 0.00163475944922 0.00858513790595
|
||||
378 4.985 0.00159244389324 0.00834234528958
|
||||
379 4.99 0.001551323598 0.00810699196376
|
||||
380 4.995 0.00151136198435 0.00787883247819
|
||||
381 5.0 0.00147252367858 0.00765763005674
|
||||
382 5.005 0.00143477446984 0.00744315627058
|
||||
383 5.01 0.00139808126924 0.00723519072448
|
||||
384 5.015 0.00136241207038 0.00703352075553
|
||||
385 5.02 0.00132773591148 0.00683794114397
|
||||
386 5.025 0.00129402283882 0.00664825383541
|
||||
387 5.03 0.00126124387159 0.00646426767408
|
||||
388 5.035 0.00122937096804 0.00628579814667
|
||||
389 5.04 0.00119837699293 0.00611266713619
|
||||
390 5.045 0.00116823568608 0.00594470268561
|
||||
391 5.05 0.00113892163217 0.00578173877069
|
||||
392 5.055 0.00111041023163 0.00562361508175
|
||||
393 5.06 0.00108267767261 0.00547017681395
|
||||
394 5.065 0.00105570090391 0.00532127446577
|
||||
395 5.07 0.00102945760901 0.00517676364527
|
||||
396 5.075 0.00100392618096 0.00503650488393
|
||||
397 5.08 0.000979085698203 0.00490036345763
|
||||
398 5.085 0.000954915901321 0.00476820921459
|
||||
399 5.09 0.000931397170562 0.00463991640989
|
||||
400 5.095 0.000908510504214 0.00451536354643
|
||||
401 5.1 0.000886237497752 0.00439443322187
|
||||
402 5.105 0.000864560323733 0.00427701198153
|
||||
403 5.11 0.000843461712415 0.00416299017686
|
||||
404 5.115 0.000822924933066 0.00405226182927
|
||||
405 5.12 0.000802933775949 0.00394472449918
|
||||
406 5.125 0.000783472534939 0.00384027916001
|
||||
407 5.13 0.000764525990765 0.00373883007694
|
||||
408 5.135 0.000746079394846 0.00364028469024
|
||||
409 5.14 0.000728118453695 0.003544553503
|
||||
410 5.145 0.000710629313879 0.00345154997304
|
||||
411 5.15 0.000693598547507 0.00336119040893
|
||||
412 5.155 0.000677013138229 0.00327339386985
|
||||
413 5.16 0.00066086046772 0.00318808206921
|
||||
414 5.165 0.000645128302652 0.00310517928183
|
||||
415 5.17 0.000629804782101 0.00302461225459
|
||||
416 5.175 0.000614878405412 0.00294631012039
|
||||
417 5.18 0.000600338020472 0.00287020431528
|
||||
418 5.185 0.000586172812398 0.00279622849864
|
||||
419 5.19 0.00057237229261 0.00272431847632
|
||||
420 5.195 0.000558926288291 0.00265441212659
|
||||
421 5.2 0.000545824932198 0.00258644932878
|
||||
422 5.205 0.000533058652834 0.00252037189458
|
||||
423 5.21 0.00052061816495 0.0024561235018
|
||||
424 5.215 0.000508494460377 0.00239364963056
|
||||
425 5.22 0.000496678799167 0.00233289750178
|
||||
426 5.225 0.000485162701041 0.00227381601795
|
||||
427 5.23 0.000473937937122 0.00221635570597
|
||||
428 5.235 0.000462996521952 0.0021604686621
|
||||
429 5.24 0.000452330705781 0.00210610849886
|
||||
430 5.245 0.000441932967112 0.00205323029391
|
||||
431 5.25 0.000431796005499 0.00200179054064
|
||||
432 5.255 0.00042191273459 0.00195174710063
|
||||
433 5.26 0.000412276275402 0.00190305915777
|
||||
434 5.265 0.000402879949816 0.00185568717402
|
||||
435 5.27 0.0003937172743 0.00180959284671
|
||||
436 5.275 0.000384781953833 0.00176473906743
|
||||
437 5.28 0.000376067876031 0.00172108988228
|
||||
438 5.285 0.000367569105476 0.00167861045357
|
||||
439 5.29 0.000359279878223 0.00163726702293
|
||||
440 5.295 0.000351194596497 0.00159702687556
|
||||
441 5.3 0.000343307823559 0.00155785830593
|
||||
442 5.305 0.000335614278743 0.00151973058449
|
||||
443 5.31 0.00032810883266 0.0014826139257
|
||||
444 5.315 0.000320786502552 0.00144647945708
|
||||
445 5.32 0.000313642447802 0.00141129918936
|
||||
446 5.325 0.000306671965594 0.00137704598769
|
||||
447 5.33 0.000299870486707 0.00134369354382
|
||||
448 5.335 0.00029323357145 0.00131121634922
|
||||
449 5.34 0.000286756905732 0.00127958966922
|
||||
450 5.345 0.00028043629725 0.00124878951793
|
||||
451 5.35 0.000274267671812 0.00121879263406
|
||||
452 5.355 0.000268247069768 0.00118957645764
|
||||
453 5.36 0.000262370642562 0.00116111910739
|
||||
454 5.365 0.000256634649393 0.00113339935902
|
||||
455 5.37 0.000251035453984 0.00110639662416
|
||||
456 5.375 0.00024556952145 0.00108009093005
|
||||
457 5.38 0.000240233415275 0.0010544628999
|
||||
458 5.385 0.000235023794375 0.00102949373396
|
||||
459 5.39 0.000229937410261 0.00100516519115
|
||||
460 5.395 0.000224971104288 0.000981459571414
|
||||
461 5.4 0.000220121804997 0.000958359698545
|
||||
462 5.405 0.000215386525533 0.000935848903702
|
||||
463 5.41 0.000210762361152 0.000913911009406
|
||||
464 5.415 0.000206246486799 0.000892530314103
|
||||
465 5.42 0.000201836154771 0.000871691577231
|
||||
466 5.425 0.000197528692444 0.000851380004787
|
||||
467 5.43 0.000193321500075 0.000831581235376
|
||||
468 5.435 0.000189212048678 0.000812281326721
|
||||
469 5.44 0.000185197877955 0.000793466742621
|
||||
470 5.445 0.000181276594303 0.000775124340337
|
||||
471 5.45 0.000177445868872 0.000757241358398
|
||||
472 5.455 0.000173703435692 0.000739805404806
|
||||
473 5.46 0.000170047089853 0.000722804445631
|
||||
474 5.465 0.000166474685742 0.000706226793976
|
||||
475 5.47 0.000162984135336 0.000690061099303
|
||||
476 5.475 0.000159573406545 0.000674296337118
|
||||
477 5.48 0.000156240521608 0.000658921798975
|
||||
478 5.485 0.000152983555536 0.000643927082819
|
||||
479 5.49 0.000149800634601 0.000629302083639
|
||||
480 5.495 0.000146689934881 0.000615036984418
|
||||
481 5.5 0.000143649680835 0.000601122247385
|
||||
482 5.505 0.00014067814393 0.000587548605543
|
||||
483 5.51 0.000137773641309 0.000574307054471
|
||||
484 5.515 0.000134934534497 0.00056138884439
|
||||
485 5.52 0.000132159228148 0.000548785472487
|
||||
486 5.525 0.000129446168827 0.000536488675478
|
||||
487 5.53 0.000126793843833 0.000524490422414
|
||||
488 5.535 0.000124200780051 0.000512782907716
|
||||
489 5.54 0.000121665542848 0.000501358544429
|
||||
490 5.545 0.000119186734991 0.000490209957694
|
||||
491 5.55 0.000116762995603 0.000479329978423
|
||||
492 5.555 0.000114392999154 0.000468711637179
|
||||
493 5.56 0.000112075454472 0.000458348158245
|
||||
494 5.565 0.000109809103791 0.000448232953884
|
||||
495 5.57 0.000107592721827 0.000438359618774
|
||||
496 5.575 0.000105425114878 0.000428721924627
|
||||
497 5.58 0.000103305119949 0.000419313814967
|
||||
498 5.585 0.000101231603912 0.000410129400077
|
||||
499 5.59 9.92034626791e-05 0.000401162952103
|
||||
500 5.595 9.72196204062e-05 0.000392408900312
|
||||
501 5.6 9.5279028721e-05 0.00038386182649
|
||||
502 5.605 9.33806659696e-05 0.000375516460498
|
||||
503 5.61 9.1523536488e-05 0.000367367675949
|
||||
504 5.615 8.97066698933e-05 0.000359410486029
|
||||
505 5.62 8.79291203961e-05 0.000351640039446
|
||||
506 5.625 8.61899661332e-05 0.000344051616503
|
||||
507 5.63 8.44883085184e-05 0.000336640625287
|
||||
508 5.635 8.28232716138e-05 0.000329402597984
|
||||
509 5.64 8.11940015174e-05 0.000322333187302
|
||||
510 5.645 7.95996657698e-05 0.000315428163002
|
||||
511 5.65 7.80394527771e-05 0.000308683408537
|
||||
512 5.655 7.65125712508e-05 0.000302094917798
|
||||
513 5.66 7.50182496635e-05 0.000295658791947
|
||||
514 5.665 7.35557357199e-05 0.000289371236362
|
||||
515 5.67 7.21242958438e-05 0.000283228557659
|
||||
516 5.675 7.07232146788e-05 0.000277227160816
|
||||
517 5.68 6.93517946035e-05 0.000271363546381
|
||||
518 5.685 6.80093552604e-05 0.000265634307756
|
||||
519 5.69 6.66952330984e-05 0.000260036128578
|
||||
520 5.695 6.5408780928e-05 0.000254565780162
|
||||
521 5.7 6.41493674892e-05 0.000249220119037
|
||||
522 5.705 6.29163770311e-05 0.000243996084541
|
||||
523 5.71 6.17092089041e-05 0.000238890696497
|
||||
524 5.715 6.05272771628e-05 0.000233901052958
|
||||
525 5.72 5.93700101809e-05 0.000229024328015
|
||||
526 5.725 5.82368502757e-05 0.000224257769672
|
||||
527 5.73 5.7127253344e-05 0.000219598697784
|
||||
528 5.735 5.6040688508e-05 0.00021504450206
|
||||
529 5.74 5.49766377708e-05 0.000210592640118
|
||||
530 5.745 5.39345956813e-05 0.000206240635602
|
||||
531 5.75 5.29140690094e-05 0.000201986076352
|
||||
532 5.755 5.19145764286e-05 0.000197826612633
|
||||
533 5.76 5.09356482089e-05 0.000193759955407
|
||||
534 5.765 4.9976825917e-05 0.000189783874667
|
||||
535 5.77 4.90376621255e-05 0.000185896197809
|
||||
536 5.775 4.811772013e-05 0.000182094808056
|
||||
537 5.78 4.72165736735e-05 0.000178377642932
|
||||
538 5.785 4.63338066786e-05 0.000174742692774
|
||||
539 5.79 4.54690129874e-05 0.00017118799929
|
||||
540 5.795 4.46217961078e-05 0.000167711654157
|
||||
541 5.8 4.37917689674e-05 0.000164311797666
|
||||
542 5.805 4.29785536734e-05 0.000160986617396
|
||||
543 5.81 4.21817812796e-05 0.000157734346936
|
||||
544 5.815 4.14010915595e-05 0.000154553264637
|
||||
545 5.82 4.06361327855e-05 0.0001514416924
|
||||
546 5.825 3.98865615139e-05 0.000148397994509
|
||||
547 5.83 3.91520423762e-05 0.000145420576481
|
||||
548 5.835 3.84322478754e-05 0.000142507883961
|
||||
549 5.84 3.77268581883e-05 0.000139658401647
|
||||
550 5.845 3.70355609728e-05 0.000136870652241
|
||||
551 5.85 3.63580511802e-05 0.000134143195433
|
||||
552 5.855 3.56940308733e-05 0.000131474626912
|
||||
553 5.86 3.5043209048e-05 0.000128863577412
|
||||
554 5.865 3.44053014612e-05 0.000126308711771
|
||||
555 5.87 3.37800304622e-05 0.000123808728033
|
||||
556 5.875 3.31671248289e-05 0.000121362356562
|
||||
557 5.88 3.25663196081e-05 0.000118968359189
|
||||
558 5.885 3.1977355961e-05 0.000116625528379
|
||||
559 5.89 3.13999810112e-05 0.000114332686424
|
||||
560 5.895 3.0833947698e-05 0.000112088684656
|
||||
561 5.9 3.02790146332e-05 0.000109892402684
|
||||
562 5.905 2.97349459611e-05 0.000107742747652
|
||||
563 5.91 2.92015112233e-05 0.000105638653516
|
||||
564 5.915 2.86784852258e-05 0.000103579080344
|
||||
565 5.92 2.81656479105e-05 0.000101563013635
|
||||
566 5.925 2.76627842296e-05 9.95894636504e-05
|
||||
567 5.93 2.71696840234e-05 9.76574647761e-05
|
||||
568 5.935 2.66861419014e-05 9.57660748914e-05
|
||||
569 5.94 2.62119571261e-05 9.39143747606e-05
|
||||
570 5.945 2.57469335003e-05 9.21014674399e-05
|
||||
571 5.95 2.52908792569e-05 9.03264777011e-05
|
||||
572 5.955 2.4843606952e-05 8.85885514709e-05
|
||||
573 5.96 2.44049333599e-05 8.68868552854e-05
|
||||
574 5.965 2.39746793724e-05 8.522057576e-05
|
||||
575 5.97 2.35526698987e-05 8.35889190733e-05
|
||||
576 5.975 2.31387337693e-05 8.19911104654e-05
|
||||
577 5.98 2.27327036419e-05 8.04263937498e-05
|
||||
578 5.985 2.23344159097e-05 7.88940308385e-05
|
||||
579 5.99 2.19437106122e-05 7.739330128e-05
|
||||
580 5.995 2.15604313477e-05 7.59235018102e-05
|
||||
581 6.0 2.1184425189e-05 7.44839459145e-05
|
||||
582 6.005 2.08155426005e-05 7.3073963403e-05
|
||||
583 6.01 2.04536373574e-05 7.16928999962e-05
|
||||
584 6.015 2.00985664675e-05 7.03401169221e-05
|
||||
585 6.02 1.97501900945e-05 6.90149905246e-05
|
||||
586 6.025 1.94083714834e-05 6.77169118817e-05
|
||||
587 6.03 1.90729768878e-05 6.64452864341e-05
|
||||
588 6.035 1.87438754988e-05 6.51995336246e-05
|
||||
589 6.04 1.84209393761e-05 6.39790865457e-05
|
||||
590 6.045 1.81040433805e-05 6.27833915977e-05
|
||||
591 6.05 1.77930651083e-05 6.16119081557e-05
|
||||
592 6.055 1.74878848271e-05 6.04641082448e-05
|
||||
593 6.06 1.71883854134e-05 5.93394762249e-05
|
||||
594 6.065 1.68944522917e-05 5.82375084831e-05
|
||||
595 6.07 1.66059733752e-05 5.71577131349e-05
|
||||
596 6.075 1.63228390077e-05 5.60996097322e-05
|
||||
597 6.08 1.60449419074e-05 5.50627289806e-05
|
||||
598 6.085 1.57721771114e-05 5.40466124625e-05
|
||||
599 6.09 1.55044419226e-05 5.30508123689e-05
|
||||
600 6.095 1.52416358567e-05 5.20748912369e-05
|
||||
601 6.1 1.49836605915e-05 5.11184216954e-05
|
||||
602 6.105 1.47304199168e-05 5.01809862165e-05
|
||||
603 6.11 1.44818196863e-05 4.92621768737e-05
|
||||
604 6.115 1.42377677693e-05 4.83615951067e-05
|
||||
605 6.12 1.39981740054e-05 4.74788514917e-05
|
||||
606 6.125 1.37629501588e-05 4.66135655183e-05
|
||||
607 6.13 1.35320098744e-05 4.57653653718e-05
|
||||
608 6.135 1.33052686347e-05 4.49338877213e-05
|
||||
609 6.14 1.30826437185e-05 4.41187775132e-05
|
||||
610 6.145 1.28640541593e-05 4.33196877704e-05
|
||||
611 6.15 1.26494207056e-05 4.25362793959e-05
|
||||
612 6.155 1.24386657825e-05 4.17682209821e-05
|
||||
613 6.16 1.22317134528e-05 4.10151886251e-05
|
||||
614 6.165 1.20284893808e-05 4.02768657433e-05
|
||||
615 6.17 1.18289207957e-05 3.95529429009e-05
|
||||
616 6.175 1.16329364562e-05 3.88431176356e-05
|
||||
617 6.18 1.14404666165e-05 3.81470942917e-05
|
||||
618 6.185 1.12514429921e-05 3.74645838561e-05
|
||||
619 6.19 1.10657987276e-05 3.67953037992e-05
|
||||
620 6.195 1.08834683642e-05 3.61389779202e-05
|
||||
621 6.2 1.07043878085e-05 3.54953361956e-05
|
||||
622 6.205 1.05284943023e-05 3.48641146318e-05
|
||||
623 6.21 1.03557263924e-05 3.42450551216e-05
|
||||
624 6.215 1.01860239019e-05 3.36379053043e-05
|
||||
625 6.22 1.00193279015e-05 3.30424184292e-05
|
||||
626 6.225 9.8555806818e-06 3.24583532225e-05
|
||||
627 6.23 9.69472572662e-06 3.18854737577e-05
|
||||
628 6.235 9.53670768611e-06 3.13235493295e-05
|
||||
629 6.24 9.38147235122e-06 3.07723543299e-05
|
||||
630 6.245 9.22896662842e-06 3.02316681289e-05
|
||||
631 6.25 9.07913851515e-06 2.97012749568e-05
|
||||
632 6.255 8.93193707577e-06 2.918096379e-05
|
||||
633 6.26 8.78731241814e-06 2.86705282402e-05
|
||||
634 6.265 8.64521567069e-06 2.81697664451e-05
|
||||
635 6.27 8.50559896007e-06 2.76784809632e-05
|
||||
636 6.275 8.36841538931e-06 2.71964786701e-05
|
||||
637 6.28 8.23361901646e-06 2.6723570658e-05
|
||||
638 6.285 8.1011648338e-06 2.62595721375e-05
|
||||
639 6.29 7.97100874743e-06 2.58043023419e-05
|
||||
640 6.295 7.84310755745e-06 2.53575844336e-05
|
||||
641 6.3 7.71741893849e-06 2.49192454134e-05
|
||||
642 6.305 7.59390142079e-06 2.44891160312e-05
|
||||
643 6.31 7.47251437163e-06 2.40670306997e-05
|
||||
644 6.315 7.35321797725e-06 2.36528274098e-05
|
||||
645 6.32 7.23597322517e-06 2.32463476478e-05
|
||||
646 6.325 7.12074188691e-06 2.28474363155e-05
|
||||
647 6.33 7.00748650108e-06 2.24559416513e-05
|
||||
648 6.335 6.89617035696e-06 2.2071715154e-05
|
||||
649 6.34 6.7867574783e-06 2.16946115076e-05
|
||||
650 6.345 6.67921260764e-06 2.1324488509e-05
|
||||
651 6.35 6.5735011909e-06 2.09612069965e-05
|
||||
652 6.355 6.46958936234e-06 2.06046307805e-05
|
||||
653 6.36 6.3674439299e-06 2.02546265761e-05
|
||||
654 6.365 6.26703236079e-06 1.99110639364e-05
|
||||
655 6.37 6.16832276753e-06 1.95738151888e-05
|
||||
656 6.375 6.07128389417e-06 1.92427553714e-05
|
||||
657 6.38 5.97588510293e-06 1.89177621723e-05
|
||||
658 6.385 5.88209636109e-06 1.85987158689e-05
|
||||
659 6.39 5.7898882282e-06 1.828549927e-05
|
||||
660 6.395 5.69923184355e-06 1.79779976587e-05
|
||||
661 6.4 5.61009891393e-06 1.76760987363e-05
|
||||
662 6.405 5.52246170172e-06 1.73796925683e-05
|
||||
663 6.41 5.43629301316e-06 1.70886715312e-05
|
||||
664 6.415 5.35156618692e-06 1.68029302607e-05
|
||||
665 6.42 5.26825508299e-06 1.6522365601e-05
|
||||
666 6.425 5.18633407167e-06 1.62468765557e-05
|
||||
667 6.43 5.105778023e-06 1.59763642392e-05
|
||||
668 6.435 5.02656229621e-06 1.57107318301e-05
|
||||
669 6.44 4.94866272963e-06 1.54498845249e-05
|
||||
670 6.445 4.87205563062e-06 1.51937294934e-05
|
||||
671 6.45 4.79671776585e-06 1.49421758345e-05
|
||||
672 6.455 4.72262635178e-06 1.4695134534e-05
|
||||
673 6.46 4.64975904529e-06 1.44525184224e-05
|
||||
674 6.465 4.57809393461e-06 1.42142421344e-05
|
||||
675 6.47 4.50760953034e-06 1.39802220687e-05
|
||||
676 6.475 4.43828475677e-06 1.37503763495e-05
|
||||
677 6.48 4.37009894334e-06 1.35246247885e-05
|
||||
678 6.485 4.30303181628e-06 1.33028888476e-05
|
||||
679 6.49 4.23706349046e-06 1.30850916027e-05
|
||||
680 6.495 4.17217446142e-06 1.28711577084e-05
|
||||
681 6.5 4.10834559754e-06 1.26610133637e-05
|
||||
682 6.505 4.04555813243e-06 1.24545862778e-05
|
||||
683 6.51 3.98379365744e-06 1.22518056372e-05
|
||||
684 6.515 3.92303411434e-06 1.20526020738e-05
|
||||
685 6.52 3.86326178824e-06 1.18569076334e-05
|
||||
686 6.525 3.8044593005e-06 1.16646557444e-05
|
||||
687 6.53 3.74660960198e-06 1.14757811888e-05
|
||||
688 6.535 3.68969596629e-06 1.12902200718e-05
|
||||
689 6.54 3.63370198326e-06 1.11079097938e-05
|
||||
690 6.545 3.57861155257e-06 1.09287890224e-05
|
||||
691 6.55 3.52440887742e-06 1.07527976647e-05
|
||||
692 6.555 3.47107845843e-06 1.05798768409e-05
|
||||
693 6.56 3.41860508767e-06 1.04099688579e-05
|
||||
694 6.565 3.36697384274e-06 1.02430171842e-05
|
||||
695 6.57 3.31617008104e-06 1.00789664243e-05
|
||||
696 6.575 3.26617943417e-06 9.91776229528e-06
|
||||
697 6.58 3.21698780242e-06 9.75935160201e-06
|
||||
698 6.585 3.16858134936e-06 9.60368221456e-06
|
||||
699 6.59 3.12094649663e-06 9.45070304518e-06
|
||||
700 6.595 3.07406991872e-06 9.30036402612e-06
|
||||
701 6.6 3.02793853796e-06 9.15261608793e-06
|
||||
702 6.605 2.98253951958e-06 9.00741113824e-06
|
||||
703 6.61 2.93786026687e-06 8.86470204097e-06
|
||||
704 6.615 2.89388841646e-06 8.72444259607e-06
|
||||
705 6.62 2.85061183368e-06 8.58658751973e-06
|
||||
706 6.625 2.80801860801e-06 8.45109242494e-06
|
||||
707 6.63 2.76609704869e-06 8.31791380259e-06
|
||||
708 6.635 2.72483568033e-06 8.18700900294e-06
|
||||
709 6.64 2.68422323868e-06 8.05833621753e-06
|
||||
710 6.645 2.64424866648e-06 7.93185446144e-06
|
||||
711 6.65 2.60490110936e-06 7.80752355606e-06
|
||||
712 6.655 2.56616991186e-06 7.6853041121e-06
|
||||
713 6.66 2.52804461354e-06 7.56515751309e-06
|
||||
714 6.665 2.49051494513e-06 7.44704589922e-06
|
||||
715 6.67 2.45357082481e-06 7.33093215148e-06
|
||||
716 6.675 2.41720235453e-06 7.21677987627e-06
|
||||
717 6.68 2.38139981644e-06 7.10455339021e-06
|
||||
718 6.685 2.34615366934e-06 6.9942177054e-06
|
||||
719 6.69 2.31145454526e-06 6.88573851497e-06
|
||||
720 6.695 2.27729324613e-06 6.7790821789e-06
|
||||
721 6.7 2.2436607404e-06 6.67421571025e-06
|
||||
722 6.705 2.21054815986e-06 6.57110676157e-06
|
||||
723 6.71 2.17794679649e-06 6.46972361177e-06
|
||||
724 6.715 2.14584809929e-06 6.3700351531e-06
|
||||
725 6.72 2.11424367135e-06 6.27201087853e-06
|
||||
726 6.725 2.08312526676e-06 6.17562086942e-06
|
||||
727 6.73 2.05248478781e-06 6.08083578334e-06
|
||||
728 6.735 2.02231428205e-06 5.98762684229e-06
|
||||
729 6.74 1.99260593955e-06 5.89596582112e-06
|
||||
730 6.745 1.96335209014e-06 5.80582503618e-06
|
||||
731 6.75 1.93454520075e-06 5.71717733423e-06
|
||||
732 6.755 1.90617787275e-06 5.62999608165e-06
|
||||
733 6.76 1.87824283942e-06 5.54425515378e-06
|
||||
734 6.765 1.85073296341e-06 5.4599289246e-06
|
||||
735 6.77 1.82364123426e-06 5.37699225653e-06
|
||||
736 6.775 1.79696076603e-06 5.29542049053e-06
|
||||
737 6.78 1.77068479486e-06 5.21518943638e-06
|
||||
738 6.785 1.74480667672e-06 5.13627536317e-06
|
||||
739 6.79 1.71931988509e-06 5.05865498999e-06
|
||||
740 6.795 1.69421800875e-06 4.98230547687e-06
|
||||
741 6.8 1.66949474959e-06 4.90720441581e-06
|
||||
742 6.805 1.6451439205e-06 4.83332982211e-06
|
||||
743 6.81 1.62115944323e-06 4.76066012583e-06
|
||||
744 6.815 1.59753534637e-06 4.68917416347e-06
|
||||
745 6.82 1.57426576334e-06 4.61885116973e-06
|
||||
746 6.825 1.55134493038e-06 4.54967076962e-06
|
||||
747 6.83 1.52876718466e-06 4.48161297055e-06
|
||||
748 6.835 1.50652696239e-06 4.41465815471e-06
|
||||
749 6.84 1.48461879691e-06 4.3487870716e-06
|
||||
750 6.845 1.46303731695e-06 4.28398083065e-06
|
||||
751 6.85 1.44177724478e-06 4.22022089406e-06
|
||||
752 6.855 1.42083339451e-06 4.15748906981e-06
|
||||
753 6.86 1.40020067034e-06 4.09576750471e-06
|
||||
754 6.865 1.37987406492e-06 4.03503867774e-06
|
||||
755 6.87 1.35984865768e-06 3.97528539342e-06
|
||||
756 6.875 1.34011961322e-06 3.91649077535e-06
|
||||
757 6.88 1.32068217977e-06 3.85863825993e-06
|
||||
758 6.885 1.30153168756e-06 3.80171159016e-06
|
||||
759 6.89 1.2826635474e-06 3.74569480958e-06
|
||||
760 6.895 1.26407324911e-06 3.69057225636e-06
|
||||
761 6.9 1.2457563601e-06 3.63632855747e-06
|
||||
762 6.905 1.22770852394e-06 3.58294862303e-06
|
||||
763 6.91 1.20992545896e-06 3.53041764074e-06
|
||||
764 6.915 1.19240295686e-06 3.47872107044e-06
|
||||
765 6.92 1.17513688137e-06 3.42784463875e-06
|
||||
766 6.925 1.15812316694e-06 3.37777433388e-06
|
||||
767 6.93 1.14135781743e-06 3.32849640049e-06
|
||||
768 6.935 1.12483690484e-06 3.27999733473e-06
|
||||
769 6.94 1.10855656808e-06 3.23226387928e-06
|
||||
770 6.945 1.09251301173e-06 3.18528301858e-06
|
||||
771 6.95 1.07670250488e-06 3.13904197413e-06
|
||||
772 6.955 1.06112137989e-06 3.09352819987e-06
|
||||
773 6.96 1.0457660313e-06 3.0487293777e-06
|
||||
774 6.965 1.03063291469e-06 3.00463341302e-06
|
||||
775 6.97 1.01571854555e-06 2.96122843043e-06
|
||||
776 6.975 1.0010194982e-06 2.9185027695e-06
|
||||
777 6.98 9.86532404745e-07 2.87644498061e-06
|
||||
778 6.985 9.72253954022e-07 2.83504382088e-06
|
||||
779 6.99 9.58180890566e-07 2.79428825018e-06
|
||||
780 6.995 9.44310013618e-07 2.75416742728e-06
|
||||
781 7.0 9.30638176135e-07 2.71467070595e-06
|
||||
782 7.005 9.17162283824e-07 2.6757876313e-06
|
||||
783 7.01 9.03879294199e-07 2.63750793605e-06
|
||||
784 7.015 8.90786215647e-07 2.59982153697e-06
|
||||
785 7.02 8.77880106517e-07 2.56271853136e-06
|
||||
786 7.025 8.6515807423e-07 2.5261891936e-06
|
||||
787 7.03 8.52617274397e-07 2.49022397175e-06
|
||||
788 7.035 8.40254909964e-07 2.4548134843e-06
|
||||
789 7.04 8.28068230364e-07 2.41994851684e-06
|
||||
790 7.045 8.16054530689e-07 2.38562001899e-06
|
||||
791 7.05 8.04211150882e-07 2.35181910119e-06
|
||||
792 7.055 7.92535474938e-07 2.3185370317e-06
|
||||
793 7.06 7.81024930121e-07 2.28576523364e-06
|
||||
794 7.065 7.696769862e-07 2.25349528197e-06
|
||||
795 7.07 7.58489154692e-07 2.22171890072e-06
|
||||
796 7.075 7.47458988133e-07 2.19042796013e-06
|
||||
797 7.08 7.36584079342e-07 2.15961447389e-06
|
||||
798 7.085 7.2586206072e-07 2.12927059646e-06
|
||||
799 7.09 7.15290603549e-07 2.09938862041e-06
|
||||
800 7.095 7.04867417307e-07 2.06996097384e-06
|
||||
801 7.1 6.94590249e-07 2.04098021782e-06
|
||||
802 7.105 6.84456882499e-07 2.01243904392e-06
|
||||
803 7.11 6.74465137898e-07 1.98433027176e-06
|
||||
804 7.115 6.64612870877e-07 1.9566468466e-06
|
||||
805 7.12 6.5489797208e-07 1.92938183703e-06
|
||||
806 7.125 6.45318366505e-07 1.90252843264e-06
|
||||
807 7.13 6.35872012904e-07 1.87607994179e-06
|
||||
808 7.135 6.26556903196e-07 1.85002978938e-06
|
||||
809 7.14 6.17371061887e-07 1.8243715147e-06
|
||||
810 7.145 6.08312545506e-07 1.7990987693e-06
|
||||
811 7.15 5.99379442048e-07 1.77420531491e-06
|
||||
812 7.155 5.90569870428e-07 1.74968502142e-06
|
||||
813 7.16 5.81881979945e-07 1.72553186483e-06
|
||||
814 7.165 5.73313949757e-07 1.70173992537e-06
|
||||
815 7.17 5.64863988364e-07 1.67830338549e-06
|
||||
816 7.175 5.56530333103e-07 1.65521652804e-06
|
||||
817 7.18 5.4831124965e-07 1.63247373439e-06
|
||||
818 7.185 5.40205031528e-07 1.61006948263e-06
|
||||
819 7.19 5.32209999637e-07 1.58799834581e-06
|
||||
820 7.195 5.24324501773e-07 1.56625499017e-06
|
||||
821 7.2 5.16546912175e-07 1.54483417343e-06
|
||||
822 7.205 5.08875631066e-07 1.52373074317e-06
|
||||
823 7.21 5.01309084211e-07 1.50293963511e-06
|
||||
824 7.215 4.93845722479e-07 1.48245587157e-06
|
||||
825 7.22 4.86484021414e-07 1.46227455985e-06
|
||||
826 7.225 4.79222480814e-07 1.44239089069e-06
|
||||
827 7.23 4.72059624319e-07 1.42280013677e-06
|
||||
828 7.235 4.64993999004e-07 1.4034976512e-06
|
||||
829 7.24 4.58024174978e-07 1.38447886607e-06
|
||||
830 7.245 4.51148744997e-07 1.36573929102e-06
|
||||
831 7.25 4.44366324079e-07 1.34727451183e-06
|
||||
832 7.255 4.37675549122e-07 1.32908018904e-06
|
||||
833 7.26 4.31075078542e-07 1.31115205663e-06
|
||||
834 7.265 4.24563591899e-07 1.29348592063e-06
|
||||
835 7.27 4.1813978955e-07 1.2760776579e-06
|
||||
836 7.275 4.11802392291e-07 1.25892321479e-06
|
||||
837 7.28 4.05550141016e-07 1.24201860594e-06
|
||||
838 7.285 3.99381796376e-07 1.22535991301e-06
|
||||
839 7.29 3.9329613845e-07 1.20894328352e-06
|
||||
840 7.295 3.87291966418e-07 1.19276492962e-06
|
||||
841 7.3 3.81368098239e-07 1.17682112698e-06
|
||||
842 7.305 3.75523370336e-07 1.16110821364e-06
|
||||
843 7.31 3.69756637291e-07 1.14562258888e-06
|
||||
844 7.315 3.64066771537e-07 1.13036071214e-06
|
||||
845 7.32 3.58452663062e-07 1.11531910195e-06
|
||||
846 7.325 3.52913219116e-07 1.10049433488e-06
|
||||
847 7.33 3.47447363922e-07 1.0858830445e-06
|
||||
848 7.335 3.42054038397e-07 1.07148192036e-06
|
||||
849 7.34 3.3673219987e-07 1.05728770703e-06
|
||||
850 7.345 3.31480821814e-07 1.04329720308e-06
|
||||
851 7.35 3.26298893574e-07 1.02950726017e-06
|
||||
852 7.355 3.21185420107e-07 1.01591478207e-06
|
||||
853 7.36 3.16139421723e-07 1.00251672378e-06
|
||||
854 7.365 3.1115993383e-07 9.89310090577e-07
|
||||
855 7.37 3.06246006687e-07 9.76291937184e-07
|
||||
856 7.375 3.01396705156e-07 9.63459366859e-07
|
||||
857 7.38 2.96611108464e-07 9.50809530558e-07
|
||||
858 7.385 2.91888309966e-07 9.38339626099e-07
|
||||
859 7.39 2.87227416913e-07 9.26046897331e-07
|
||||
860 7.395 2.82627550221e-07 9.13928633336e-07
|
||||
861 7.4 2.78087844251e-07 9.01982167635e-07
|
||||
862 7.405 2.73607446588e-07 8.90204877406e-07
|
||||
863 7.41 2.6918551782e-07 8.78594182731e-07
|
||||
864 7.415 2.64821231333e-07 8.67147545837e-07
|
||||
865 7.42 2.60513773095e-07 8.55862470371e-07
|
||||
866 7.425 2.56262341455e-07 8.44736500673e-07
|
||||
867 7.43 2.5206614694e-07 8.33767221072e-07
|
||||
868 7.435 2.47924412057e-07 8.22952255188e-07
|
||||
869 7.44 2.43836371097e-07 8.12289265255e-07
|
||||
870 7.445 2.39801269946e-07 8.01775951447e-07
|
||||
871 7.45 2.35818365896e-07 7.91410051224e-07
|
||||
872 7.455 2.31886927457e-07 7.81189338689e-07
|
||||
873 7.46 2.28006234181e-07 7.7111162395e-07
|
||||
874 7.465 2.2417557648e-07 7.61174752504e-07
|
||||
875 7.47 2.20394255452e-07 7.51376604623e-07
|
||||
876 7.475 2.16661582706e-07 7.41715094759e-07
|
||||
877 7.48 2.12976880196e-07 7.32188170953e-07
|
||||
878 7.485 2.09339480053e-07 7.22793814262e-07
|
||||
879 7.49 2.05748724421e-07 7.13530038185e-07
|
||||
880 7.495 2.02203965296e-07 7.04394888118e-07
|
||||
881 7.5 1.9870456437e-07 6.95386440797e-07
|
||||
882 7.505 1.95249892873e-07 6.86502803769e-07
|
||||
883 7.51 1.91839331421e-07 6.77742114863e-07
|
||||
884 7.515 1.88472269866e-07 6.69102541673e-07
|
||||
885 7.52 1.85148107151e-07 6.60582281052e-07
|
||||
886 7.525 1.8186625116e-07 6.52179558612e-07
|
||||
887 7.53 1.7862611858e-07 6.43892628236e-07
|
||||
888 7.535 1.75427134757e-07 6.35719771598e-07
|
||||
889 7.54 1.72268733561e-07 6.27659297689e-07
|
||||
890 7.545 1.6915035725e-07 6.19709542357e-07
|
||||
891 7.55 1.66071456337e-07 6.11868867849e-07
|
||||
892 7.555 1.63031489458e-07 6.04135662368e-07
|
||||
893 7.56 1.60029923244e-07 5.96508339628e-07
|
||||
894 7.565 1.57066232194e-07 5.88985338432e-07
|
||||
895 7.57 1.54139898552e-07 5.81565122242e-07
|
||||
896 7.575 1.51250412185e-07 5.74246178766e-07
|
||||
897 7.58 1.48397270459e-07 5.6702701955e-07
|
||||
898 7.585 1.45579978125e-07 5.59906179576e-07
|
||||
899 7.59 1.42798047202e-07 5.52882216872e-07
|
||||
900 7.595 1.40050996861e-07 5.4595371212e-07
|
||||
901 7.6 1.37338353314e-07 5.39119268281e-07
|
||||
902 7.605 1.34659649703e-07 5.32377510221e-07
|
||||
903 7.61 1.32014425993e-07 5.25727084341e-07
|
||||
904 7.615 1.29402228861e-07 5.19166658223e-07
|
||||
905 7.62 1.26822611598e-07 5.12694920274e-07
|
||||
906 7.625 1.24275133998e-07 5.06310579376e-07
|
||||
907 7.63 1.21759362262e-07 5.0001236455e-07
|
||||
908 7.635 1.19274868896e-07 4.93799024619e-07
|
||||
909 7.64 1.16821232612e-07 4.87669327877e-07
|
||||
910 7.645 1.14398038233e-07 4.8162206177e-07
|
||||
911 7.65 1.120048766e-07 4.75656032572e-07
|
||||
912 7.655 1.09641344473e-07 4.69770065082e-07
|
||||
913 7.66 1.07307044442e-07 4.63963002309e-07
|
||||
914 7.665 1.05001584841e-07 4.58233705177e-07
|
||||
915 7.67 1.02724579651e-07 4.52581052224e-07
|
||||
916 7.675 1.0047564842e-07 4.47003939317e-07
|
||||
917 7.68 9.82544161708e-08 4.41501279361e-07
|
||||
918 7.685 9.60605133226e-08 4.36072002025e-07
|
||||
919 7.69 9.38935756035e-08 4.30715053459e-07
|
||||
920 7.695 9.17532439703e-08 4.25429396028e-07
|
||||
921 7.7 8.96391645283e-08 4.20214008047e-07
|
||||
922 7.705 8.75509884516e-08 4.15067883513e-07
|
||||
923 7.71 8.54883719059e-08 4.09990031857e-07
|
||||
924 7.715 8.34509759714e-08 4.04979477684e-07
|
||||
925 7.72 8.14384665682e-08 4.00035260529e-07
|
||||
926 7.725 7.94505143815e-08 3.95156434615e-07
|
||||
927 7.73 7.74867947896e-08 3.90342068606e-07
|
||||
928 7.735 7.55469877916e-08 3.85591245382e-07
|
||||
929 7.74 7.36307779372e-08 3.80903061797e-07
|
||||
930 7.745 7.17378542573e-08 3.76276628463e-07
|
||||
931 7.75 6.9867910196e-08 3.71711069515e-07
|
||||
932 7.755 6.80206435432e-08 3.67205522401e-07
|
||||
933 7.76 6.61957563687e-08 3.62759137662e-07
|
||||
934 7.765 6.43929549576e-08 3.5837107872e-07
|
||||
935 7.77 6.26119497457e-08 3.54040521671e-07
|
||||
936 7.775 6.08524552575e-08 3.49766655078e-07
|
||||
937 7.78 5.91141900435e-08 3.45548679773e-07
|
||||
938 7.785 5.73968766201e-08 3.41385808656e-07
|
||||
939 7.79 5.57002414093e-08 3.37277266505e-07
|
||||
940 7.795 5.402401468e-08 3.33222289779e-07
|
||||
941 7.8 5.23679304898e-08 3.29220126433e-07
|
||||
942 7.805 5.07317266285e-08 3.25270035737e-07
|
||||
943 7.81 4.91151445613e-08 3.21371288087e-07
|
||||
944 7.815 4.75179293742e-08 3.17523164833e-07
|
||||
945 7.82 4.59398297194e-08 3.13724958102e-07
|
||||
946 7.825 4.43805977617e-08 3.09975970624e-07
|
||||
947 7.83 4.28399891263e-08 3.06275515564e-07
|
||||
948 7.835 4.13177628469e-08 3.02622916355e-07
|
||||
949 7.84 3.98136813144e-08 2.99017506534e-07
|
||||
950 7.845 3.83275102273e-08 2.95458629582e-07
|
||||
951 7.85 3.68590185422e-08 2.91945638765e-07
|
||||
952 7.855 3.54079784251e-08 2.8847789698e-07
|
||||
953 7.86 3.39741652039e-08 2.85054776599e-07
|
||||
954 7.865 3.25573573211e-08 2.81675659322e-07
|
||||
955 7.87 3.11573362879e-08 2.78339936025e-07
|
||||
956 7.875 2.97738866382e-08 2.7504700662e-07
|
||||
957 7.88 2.84067958844e-08 2.71796279909e-07
|
||||
958 7.885 2.70558544725e-08 2.68587173443e-07
|
||||
959 7.89 2.57208557397e-08 2.65419113385e-07
|
||||
960 7.895 2.44015958707e-08 2.62291534374e-07
|
||||
961 7.9 2.30978738564e-08 2.59203879393e-07
|
||||
962 7.905 2.18094914519e-08 2.56155599635e-07
|
||||
963 7.91 2.05362531363e-08 2.53146154374e-07
|
||||
964 7.915 1.92779660724e-08 2.50175010842e-07
|
||||
965 7.92 1.8034440067e-08 2.47241644098e-07
|
||||
966 7.925 1.68054875325e-08 2.44345536912e-07
|
||||
967 7.93 1.55909234484e-08 2.41486179638e-07
|
||||
968 7.935 1.43905653237e-08 2.38663070101e-07
|
||||
969 7.94 1.32042331597e-08 2.35875713474e-07
|
||||
970 7.945 1.20317494138e-08 2.33123622171e-07
|
||||
971 7.95 1.08729389636e-08 2.30406315726e-07
|
||||
972 7.955 9.72762907123e-09 2.27723320689e-07
|
||||
973 7.96 8.59564934896e-09 2.2507417051e-07
|
||||
974 7.965 7.47683172465e-09 2.2245840544e-07
|
||||
975 7.97 6.37101040818e-09 2.19875572416e-07
|
||||
976 7.975 5.27802185823e-09 2.17325224966e-07
|
||||
977 7.98 4.19770474957e-09 2.148069231e-07
|
||||
978 7.985 3.12989994095e-09 2.12320233213e-07
|
||||
979 7.99 2.07445044336e-09 2.09864727985e-07
|
||||
980 7.995 1.03120138888e-09 2.07439986287e-07
|
||||
981 8.0 0.0 0.0
|
||||
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
@ -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
|
||||
@ -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
|
||||
|
||||
@ -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 ../
|
||||
@ -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.)
|
||||
@ -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
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 23 KiB |
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user