run.in.nvt
7b5385eac6bblammps-icms

run.in.nvt
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			# -- Init Section --

			include system.in.init

			# -- Atom Definition Section --

			# I you want to be careful, you can minimize the system first. (Try using
			# "run.in.min" and uncomment the read_restart command in this file below.)
			# read_restart system_after_min.rst

			read_data system.data

			# -- Settings Section --

			include system.in.settings

			# -- Run Section --


			timestep 0.025
			dump 1 all custom 50 traj_nvt.lammpstrj id mol type x y z ix iy iz

			# To use Langevin dynamics in LAMMPS you need both "fix langevin" and "fix nve".
			# (See http://lammps.sandia.gov/doc/fix_langevin.html for details.)

			# Keep the chaperonin fixed. Only let the protein move.

			fix fxlan proteins langevin 0.39 0.39 1.0 48279
			fix fxnve proteins nve

			# Notes:
			# The temperature is in reduced units and is set to 0.39
			# which is the folding temperature for the unfrustrated protein.
			# The inverse-damping-rate "damp" (which has units of time) is set to 1.0,
			# as it was in the paper. (Hopefully folding times should be similar.)
			# (See http://lammps.sandia.gov/doc/fix_langevin.html)


			thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
			thermo_modify norm no #(report total energy not energy / num_atoms)
			thermo 50 #(time interval for printing out "thermo" data)

			#restart 100000000 restart_nvt

			run 5000

			write_restart system_after_nvt.rst