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# 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 ../
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