README_setup.sh
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README_setup.sh
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			# 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.
			# Move them to the directory where you plan to run LAMMPS (in this case "../")
			mv -f system.data system.in* ../

			# 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 ../


			# Optional:
			# Note: The system.data and system.in.settings files contain extra information
			# for atoms defined in GAFF which you are not using in this simulation. This
			# is harmless, but if you to delete this information from your
			# system.in.settings and system.in.data files, follow the instructions in
			# this script: "optional_cleanup/README_remove_irrelevant_info.sh"