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lammps/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/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):
# Create LAMMPS input files this way:
cd moltemplate_files
# First, rescale and interpolate the positions
# where the monomers will be located. (This step is
# not needed if the coords_orig.raw file already has correct coordinates.)
./interpolate_coords.py 32768 1.6198059 < coords_orig.raw > coords.raw
# Then, build the "system.lt" file
./generate_system_lt.py 32768 51 < coords.raw > system.lt
# 32768 is the number of monomers in the polymer
# (which may be different from the number of coordinates
# in the "coords_orig.raw" file) This number will vary
# depending on how long you want the polymer to be.
# The second argument "51" is the average interval between
# condensin anchors (IE the "loop size" in monomers.)
# Run moltemplate
moltemplate.sh system.lt -a "@bond:stage1 1" \
-a "@bond:stage2 2" \
-a "@atom:Monomer/A 1"
# 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).
#
# We used the "-a" command to set the variable @bond:condensin to "2"
# because we will refer to it later in the "run.in" LAMMPS input script.
# (Of coarse, LAMMPS knows nothing about moltemplate variables,
# so in that file we refer to it as dihedral type "1")
mv -f system.in* system.data ../
# We also need the table of bond forces used during "stage 2".
# (Like the system.data and the various input scripts, this file is needed by
# LAMMPS, so we need to copy it to the directory where we will run the sim.)
cp -f table_bonds_stage2.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/
# Optional:
# Remove the "system.lt" file created by "generate_system_lt.py"
#rm -f system.lt
cd ../
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