run.in.npt
3f68d370b505lammm-devel

run.in.npt
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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.)

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

			include system.in.init

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

			read_data system.data

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

			include system.in.settings

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


			# -- minimization protocol --

			# Note: The minimization step is not necessary in this example. However
			# in general, it's always a good idea to minimize the system beforehand.
			# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
			unfix fShakeSPCE
			minimize 1.0e-3 1.0e-5 100000 400000
			# Now read "system.in.settings" in order to redefine fShakeSPCE again:
			include system.in.settings

			# -- simulation protocol --


			timestep 1.0
			dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
			fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
			thermo 100

			run 10000

			# Now that the system's temperature has become more equilibrated,
			# we can increase the timestep:

			timestep 2.0
			run 50000

			write_data system_after_npt.data