run.in.nvt
3f68d370b505master

run.in.nvt
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			# PREREQUISITES:
			#
			# 1) You must use moltemplate.sh to create 3 files:
			# system.data system.in.init system.in.settings
			# (Follow the instructions in README_setup.sh,
			# or run the file as a script using ./README_setup.sh)
			# 2) You must equilibrate the system beforehand using "run.in.npt".
			# This will create the file "system_after_npt.data" which this file reads.
			# (Note: I have not verified that this equilibration protocol works well.)

			# ------------------------------- Initialization Section --------------------

			include "system.in.init"

			# ------------------------------- Atom Definition Section -------------------

			# Read the coordinates generated by an earlier NPT simulation

			read_data "system_after_npt.data"

			# ------------------------------- Settings Section --------------------------

			include "system.in.settings"


			# (The "write_restart" and "read_restart" commands were buggy in 2012,
			# but they should work also. I prefer "write_data" and "read_data".)

			# ------------------------------- Settings Section --------------------------

			include system.in.settings

			# ------------------------------- Run Section -------------------------------

			# -- simulation protocol --


			timestep 1.0
			dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz
			fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
			thermo 500
			#thermo_modify flush yes

			run 200000

			write_data system_after_nvt.data