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lammps/tools/moltemplate/examples/coarse_grained/membrane_BranniganPRE2005/moltemplate_files/system.lt
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# 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)
#
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