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lammps/tools/moltemplate/examples/force_field_AMBER/waterTIP3P+isobutane/run.in.nvt
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run.in.nvt
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# PREREQUISITES:
#
# 1) You must use moltemplate.sh to create 3 files:
# system.data system.in.init system.in.settings
# (Follow the instructions in README_setup.sh,
# or run the file as a script using ./README_setup.sh)
# 2) You must equilibrate the system beforehand using "run.in.npt".
# This will create the file "system_after_npt.data" which this file reads.
# (Note: I have not verified that this equilibration protocol works well.)
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
# Read the coordinates generated by an earlier NPT simulation
read_data system_after_npt.data
# (The "write_restart" and "read_restart" commands were buggy in 2012,
# but they should work also. I prefer "write_data" and "read_data".)
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# COMMENTING OUT MINIMIZATION STEPS:
# If you are reading the coordinates generated by the NPT run
# then you should not need to minimize the system beforehand.
# -- minimization protocol --
## ("fix shake" is incompatible with "minimize".)
#unfix fShakeTIP3P
#minimize 1.0e-4 1.0e-6 100000 400000
## Now read "system.in.settings" in order to redefine fShakeTIP3P again:
#include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
thermo 500
#thermo_modify flush yes
run 50000
write_data system_after_nvt.data
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