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lammps/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/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 restart file "system_after_npt.rst" with reasonable
# coordinates at that temperature and pressure. Then we could load it now:
#
#read_restart system_after_npt.rst
#
# Unfortunately the LAMMPS "read_restart" command has been undependable over
# the past year (2012), and I feel it is safer to remove it from the examples.
# Instead, for this example, I just read the raw coordinates generated by
# moltemplate (and the default volume). (I get fewer questions this way.)
# However you should never run any liquid simulations at constant volume without
# pressure equilibration first. Hopefully in the future "read_restart" will
# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
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.
# fSHAKE was defined in system.in.settings. It is incompatible with "minimize".
unfix fSHAKE
minimize 1.0e-5 1.0e-7 100000 400000
# Now read "system.in.settings" in order to redefine fSHAKE 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
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
write_restart system_after_nvt.rst
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