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

			# 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 ../

			# 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 ../