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lammps/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/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 -------------------------------
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_restart system_after_nvt.rst
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