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lammps/tools/moltemplate/examples/CG_biomolecules/vesicle_PACKMOL/moltemplate_files/system.lt
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# Description:
#
# This example shows how to build a multicomponent spherical vesicle.
# The lipid bilayer is composed of two different lipids (DPPC and DLPC),
# The vesicle contains 120 trans-membrane protein inclusions.
#
# The DPPC lipid model is described here:
# G. Brannigan, P.F. Philips, and F.L.H. Brown,
# Physical Review E, Vol 72, 011915 (2005)
# The protein model is described here:
# G. Bellesia, AI Jewett, and J-E Shea,
# Protein Science, Vol19 141-154 (2010)
# The new DLPC model is a truncated version of DPPC,
# (Its behaviour has not been rigorously tested.)
# Note that 50%/50% mixtures of DPPC & DLPC are commonly used to
# build liposomes http://www.ncbi.nlm.nih.gov/pubmed/10620293
#
# NOTE: THE COORDINATES FOR THESE MOLECULES ARE GENERATED BY PACKMOL (see below)
#
# NOTE:
# This example may require additional features to be added to LAMMPS.
# If LAMMPS complains about an "Invalid pair_style", then copy the code
# in the "additional_lammps_code" directory into your LAMMPS "src" directory
# and recompile LAMMPS.
# First, load the definitions of the molecules we will need:
import "CGLipidBr2005.lt"
using namespace CGLipidBr2005
import "1beadProtSci2010.lt"
using namespace 1beadProtSci2010
# PREREQUISITES:
# Coordinates for the molecules in this example are loaded from an .XYZ file
# created by PACKMOL. This must be done in advance. (See ../packmol_files/)
#
# The XYZ file was created by PACKMOL in 3 steps:
# (Add the proteins, then pack lipids in the inner & outer layers around them.)
#
# step1) Creae 120 proteins. Distribute them on the surface of the sphere.
#
# step2) Keeping the coordinates from step1 fixed,
# a) first we add 9500 DPPC lipids to the inner monolayer
# b) then we add 9500 DLPC lipids to the inner monolayer
#
# step3) Keeping the coordinates from steps 1 and 2 fixed,
# a) first we add 12500 DPPC lipids to the outer monolayer
# b) then we add 12500 DLPC lipids to the outer monolayer
#
# The order that molecules are created in moltemplate should match the order
# they appear in the final XYZ file created by PACKMOL. (See above.)
# Consequently I instantiate the molecules in the same order here:
# Step 1) ---- protein inclusions ----
proteins = new 4HelixInsideOut [120]
# Step 2a) ---- inner monolayer ----
dppc_in = new DPPC [9500]
# Step 2b)
dlpc_in = new DLPC [9500]
# Step 3a) ---- outer monolayer ----
dppc_out = new DPPC [12500]
# Step 3b)
dlpc_out = new DLPC [12500]
# ------------------ boundary conditions --------------------
write_once("Data Boundary") {
-500.0 500.0 xlo xhi
-500.0 500.0 ylo yhi
-500.0 500.0 zlo zhi
}
write_once("In Settings") {
# -----------------------------------------------------------
# -------- interactions between protein and lipids ----------
# -----------------------------------------------------------
# Interactions between the protein and lipid atoms are usually
# determined by mixing rules. (However this is not possible some
# for atoms, such as the "int" atoms in the lipid model which
# interact using -1/r^2 attraction.) Mixing rules do not make
# sense for these atoms so we must explicitly define their
# interaction with all other atoms.
# We want the hydrophobic interactions between hydrophobic residues in
# the protein and beads the interior of the lipid to be energetically
# similar to the attractive interactions between the lipid tails.
#
# Note: I made the width of the outward-facing protein beads slightly larger
# ("12.5") whenever they interact with the "tail" beads in each lipid
# (in order to make the protein wider there).
# This hopefully relieves some of the internal negative pressure in the center
# of the bilayer which can otherwise rip apart the protein or suck it into
# the bilaer. (This is a hack, and I'm not sure if it is necessary.
# For different protein or lipid models, you probably don't need this.)
#
# i j pairstylename eps sig K L
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 12.5 0.4 -1
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 -1
# To help keep the protein from tilting 90 degrees and burying itself
# within the lipid bilayer, we make the turn regions at either
# end of the protein (strongly) attracted to the head groups
# of the lipid. (In reality, they would probably be attracted
# to the water as well.)
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
# All other interactions between proteins and lipids are steric.
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/tail @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/int @atom:1beadProtSci2010/tN lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DPPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
pair_coeff @atom:CGLipidBr2005/DLPC/head @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 0.1643 7.5 0.4 0
# -----------------------------------------------------------
# -------- Modifications to the protein model: --------------
# -----------------------------------------------------------
#
# Turn off attraction between the hydrophobic "@atom:sH" beads:
# (These beads are located in the outside of a trans-membrane protein.)
pair_coeff @atom:1beadProtSci2010/sH @atom:1beadProtSci2010/sH lj/charmm/coul/charmm/inter 1.8065518 5.5 1 0
# (Why: These beads are only attracted to
# each other in an aqueous environment)
# ... and
# Turn ON attraction between the hydrophilic "@atom:sL" beads.
# (These beads are located in the interior of a trans-membrane protein.)
pair_coeff @atom:1beadProtSci2010/sL @atom:1beadProtSci2010/sL lj/charmm/coul/charmm/inter 1.8065518 5.5 1 -1
# Why?
# In reality, polar groups in the interior of trans-membrane
# proteins do form hydrogen bonds with each other. This was
# absent from the original protein model because, in an aqueous
# environment, these groups preferentially interact with the water.
#
# Why is this necessary?
# Shouldn't attraction between lipid tails and the protein create
# an effective force which brings the hydrophilic beads together?
# (similar to the hydrophobic effect, but in reverse?).
# Answer:
# Unlike an aqueous environment (~zero pressure, or +1atm), there is
# a large negative pressure in the interior of some bilayer membrane
# models (such as this one). Without some kind of direct attraction
# between interior residues, the protein will get pulled apart.
# (Perhaps the attractive force I am using is too strong?)
}
# Finally, we must combine the two force-field styles which were used for
# the coarse-grained lipid and protein. To do that, we write one last time
# to the "In Init" section. When reading the "Init" section LAMMPS will
# read these commands last and this will override any earlier settings.
write_once("In Init") {
# -- These styles override earlier settings --
units real
atom_style full
# (Hybrid force field styles were used for portability.)
bond_style hybrid harmonic
angle_style hybrid cosine/delta harmonic
dihedral_style hybrid fourier
improper_style none
pair_style hybrid table linear 1130 lj/charmm/coul/charmm/inter es4k4l 14.5 15
pair_modify mix arithmetic
special_bonds lj 0.0 0.0 1.0 # turn off pairs if "less than 3 bonds"
communicate multi
}
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