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lammps/tools/moltemplate/examples/coarse_grained_examples/abstract_translocation/run.in.npt
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# -- Init Section --
include system.in.init
# -- Atom Definition Section --
read_data system.data
# -- Settings Section --
include system.in.settings
# -- Run Section --
timestep 1.0
dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
velocity groupB zero angular
velocity groupB zero linear
# (I'm not sure if the two lines above are necessary, but they don't hurt.)
# Only the groupB atoms are immobile.
group mobile subtract all groupB
# ------------------------- NPT ---------------------------
# Set temp=300K, pressure=500bar, and equilibrate volume only in the z direction
fix fMoveStuff mobile npt temp 300 300 100 z 500 500 1000.0 dilate mobile
# ------ QUESTIONABLE (see below): ------
fix Ffreezestuff groupB rigid/npt single temp 300 300 100 z 500 500 1000.0 force * off off off torque * off off off dilate mobile
# -- Alternate npt rigid method --
# I'm not sure which way is more correct, however
# this also seems to behave in a reasonable-looking way:
#fix Ffreezestuff groupB rigid single force * off off off torque * off off off dilate mobile
#
# The use of either "fix rigid" or "fix rigid/npt" to immobilize
# an object is somewhat controversial. Feel free to omit it.
#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing
#molecules, but I noticed that at NPT, it does a better job of maintaining
# the correct volume. However "fix rigid" has changed since then (2011),
# so this may no longer be true. Please use this example with caution.)
# ----------------------------------------
# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the
# forces between immobilized atoms.
neigh_modify exclude group groupB groupB
# The next two lines recalculate the temperature
# using only the mobile degrees of freedom:
compute tempMobile mobile temp
compute pressMobile all pressure tempMobile
thermo_style custom step c_tempMobile c_pressMobile temp press vol
fix_modify fMoveStuff temp tempMobile
run 60000
write_data system_after_npt.data
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