Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/tools/moltemplate/examples/coarse_grained/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/system.lt
12150ffa7397lammm-devel

Last Change
Raw File

system.lt
View Options

# Description:
#
# This example shows how to build a multicomponent spherical vesicle.
# The lipid bilayer is composed of two different lipids (DPPC and DLPC),
# The vesicle contains 120 trans-membrane protein inclusions.
#
# The DPPC lipid model is described here:
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
# Physical Review E, Vol 72, 011915 (2005)
# The protein model is described here:
# G. Bellesia, AI Jewett, and J-E Shea,
# Protein Science, Vol19 141-154 (2010)
# The new DLPC model is a truncated version of DPPC,
# (Its behaviour has not been rigorously tested.)
# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
#
# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below)
#
# NOTE:
# This example may require additional features to be added to LAMMPS.
# If LAMMPS complains about an "Invalid pair_style", then copy the code
# in the "additional_lammps_code" directory into your LAMMPS "src" directory
# and recompile LAMMPS.
# First, load the definitions of the molecules we will need:
import "CGLipidBr2005.lt"
using namespace CGLipidBr2005
import "1beadProtSci2010.lt"
using namespace 1beadProtSci2010
# PREREQUISITES:
# Coordinates for the molecules in this example are loaded from an .XYZ file
# created by PACKMOL. This must be done in advance. (See ../packmol_files/)
#
# The XYZ file was created by PACKMOL in 3 steps:
# (Add the proteins, then pack lipids in the inner & outer layers around them.)
#
# step1) Creae 120 proteins. Distribute them on the surface of the sphere.
#
# step2) Keeping the coordinates from step1 fixed,
# a) first we add 9500 DPPC lipids to the inner monolayer
# b) then we add 9500 DLPC lipids to the inner monolayer
#
# step3) Keeping the coordinates from steps 1 and 2 fixed,
# a) first we add 12500 DPPC lipids to the outer monolayer
# b) then we add 12500 DLPC lipids to the outer monolayer
#
# The order that molecules are created in moltemplate should match the order
# they appear in the final XYZ file created by PACKMOL. (See above.)
# Consequently I instantiate the molecules in the same order here:
# Step 1) ---- protein inclusions ----
proteins = new 4HelixInsideOut [120]
# Step 2a) ---- inner monolayer ----
dppc_in = new DPPC [9500]
# Step 2b)
dlpc_in = new DLPC [9500]
# Step 3a) ---- outer monolayer ----
dppc_out = new DPPC [12500]
# Step 3b)
dlpc_out = new DLPC [12500]
# ------------------ boundary conditions --------------------
write_once("Data Boundary") {
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi
}
# -------- interactions between protein and lipids ----------
# Note: All atom types must include the full path (the name of
# the namespace which defined them as well as the atom type name).
# (This is because we are no longer inside that namespace.)
write_once("In Settings") {
# Interactions between the protein and lipid atoms are usually
# determined by mixing rules. However this is not possible some
# for atoms (such as the "int" atoms in the lipid model which
# interact using -1/r^2 attraction). Lorentz-Berthelot mixing
# rules do not make sense for these atoms so we must explicitly
# define their interaction with all other atoms.
# i j pairstylename eps sig K L
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
# We want the interactions between hydrophobic residues and atoms in
# the interior of the lipid to be energetically similar to the attractive
# interactions between hydrophobic residues. (See 1beadProtSci2010.)
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 -1
# All other interactions between proteins and lipids are steric.
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 7.5 1 0
# We also add an artificial attractive interaction between the
# turn residues of the protein and the lipid head groups in
# order to keep the protein upright. This might not be necessary
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 6.0 1 -1
# Add a weak attractive interaction between hydrophilic "sL" beads
# (Whose strength mimics the strength of interaction between tail beads
# in the lipid. This was absent from the original protein model.
# However without some kind of weak attraction between residues,
# the negative pressure in the interior of the bilayer membrane
# allways pulls the protein apart. Recall that in the membrane,
# the hydrophobic beads in the protein will face outwards towards the lipid
# tails leaving the hydrophilic amino acids of the protein in the interior.
# In reality, these polar groups form hydrogen bonds with each other.)
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.3286 6.0 0.4 -1
# However these hydrophilic amino acids are not attracted to
# the bilayer interior.
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
}
# Finally, we must combine the two force-field styles which were used for
# the coarse-grained lipid and protein. To do that, we write one last time
# to the "In Init" section. When reading the "Init" section LAMMPS will
# read these commands last and this will override any earlier settings.
write_once("In Init") {
# -- These styles override earlier settings --
units real
atom_style full
# (Hybrid force field styles were used for portability.)
bond_style hybrid harmonic
angle_style hybrid cosine/delta harmonic
dihedral_style hybrid fourier
improper_style none
pair_style hybrid table linear 1001 lj/charmm/coul/charmm/inter es4k4l 14.5 15
pair_modify mix arithmetic
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
}
c4science · Help