run.in.npt
9a0e9670fb05lammm-devel

run.in.npt
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			# -------- REQUIREMENTS: ---------
			# 1) This example may require additional features and bug fixes for LAMMPS.
			# Be sure to download and copy the "additional_lammps_code" from
			# http://moltemplate.org (upper-left corner menu)
			# 2) Unpack it
			# 3) copy the .cpp and .h files to the src folding of your lammps installation.
			# 4) Compile LAMMPS.
			#
			# (If LAMMPS complains about an "Invalid pair_style"
			# then you made a mistake in the instructions above.)
			#

			# -- Init Section --

			include system.in.init

			# -- Atom Definition Section --

			read_data system.data

			# -- Settings Section --

			include system.in.settings

			# -- Run Section --


			timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
			dump 1 all custom 10000 traj_npt.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 fxnph all nph x 0 0 1000 y 0 0 1000

			# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
			# for the "epsilon" used by the coarse-grained lipid.
			# Note: The langevin damping parameter "120" corresponds to
			# the 0.12ps damping time used in Watson et. al JCP 2011.
			# Note: We maintain the system system at constant (zero) tention
			# using a barostat damping parameter Pdamp=1000 ("0 0 1000")


			# optional (not sure if this helps):
			# balance x uniform y uniform


			#restart 1000000

			run 2000000

			write_restart system_after_npt.rst