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lammps/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/README_setup.sh
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README_setup.sh
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# Use these commands to generate the LAMMPS input script and data file
# (and other auxilliary files):
# First, generate the coordinates (the "system.xyz" file) this way
# (This can be a very slow process.)
cd packmol_files
# You must run each packmol commend one after the other
# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding
# "inp" file. This should not happen. You can also usually interrupt
# packmol after 30 minutes, and the solution at that point should be good
# enough for use.
packmol < step1_proteins.inp # This step determines the protein's location
# It takes ~20 minutes (on an intel i7)
packmol < step2_innerlayer.inp # this step builds the inner monolayer
# It takes ~90 minutes
packmol < step3_outerlayer.inp # this step builds the outer monolayer
# It takes ~4 hours
# Running these three commands will probably take about an hour.
# (It depends on how uniformly you need the packing to be.)
mv -f step3_outerlayer.xyz ../system.xyz
cd ..
# Create LAMMPS input files this way:
cd moltemplate_files
# run moltemplate
moltemplate.sh -xyz ../system.xyz 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 ../
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