run.in.nvt
775e8f3cc8f5lammm-master-deprecated

run.in.nvt
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			# ------------------------------- Initialization Section --------------------

			include system.in.init

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


			# Normally, I would minimize the system and equilibrate the system at constant
			# pressure and temperature beforehand. If you run lammps with "run.in.npt",
			# it will generate a data file "system_after_npt.data" with reasonable
			# coordinates at that temperature and pressure. Then we could load it now:
			#
			#read_data system_after_npt.data

			read_data system.data

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

			include system.in.settings

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


			timestep 6.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
			dump 1 all custom 5000 traj_nvt.lammpstrj id mol type x y z ix iy iz


			thermo_style custom step temp pe etotal vol epair ebond eangle
			thermo 1000 # time interval for printing out "thermo" data


			fix fxlan all langevin 300.0 300.0 120 48279
			fix fxnve all nve

			# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
			# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
			# Note: The langevin damping parameter "120" corresponds to
			# the 0.12ps damping time used in Watson et. al JCP 2011.

			#restart 1000000

			run 1000000

			write_data system_after_nvt.data