run.in.nvt
16eed7a05366efficient_neuronet

run.in.nvt
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			# PREREQUISITES:
			#
			# You must use moltemplate.sh to create 3 files:
			# system.data system.in.init system.in.settings
			# (See README_setup.sh for details)

			# -- Init Section --

			include system.in.init

			# -- Atom Definition Section --

			read_data system.data

			# -- Settings Section --

			include system.in.settings

			# -- Run Section --


			timestep 1.0
			dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz

			thermo_style custom step temp pe etotal vol epair ebond eangle edihed
			thermo 500 # time interval for printing out "thermo" data


			# Optional: Improve efficiency by omitting the calcuation of interactions
			# between immobile atoms. (Note: This is not optional under NPT conditions.)
			neigh_modify exclude group groupB groupB

			# Only the groupB atoms are immobile.
			group mobile subtract all groupB

			# The next two lines recalculate the temperature
			# using only the mobile degrees of freedom:

			compute tempMobile mobile temp

			# Integrate the equations of motion:
			fix fMoveStuff mobile nvt temp 300.0 300.0 100.0
			fix_modify fMoveStuff temp tempMobile


			run 100000

			write_data system_after_nvt.data