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lammps/tools/moltemplate/examples/coarse_grained/3bodyWater+hydrocarbons_MW+TraPPE/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
# (See README_setup.sh for details.)
# 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.)
# run.in.nvt
#
# -- Usage --
#
# lmp_g++ -i run.in.nvt
# (assuming lmp_g++ is the name of your lammps binary)
#
# -- Prerequisite Input Files: --
# systen.data, system.in.init, system.in.settings, system.in.sw
# system_after_npt.data
#
# You can generate these files using this procedure
#
# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
#
# lmp_linux -i run.in.npt
# ---------------------------------
# -- init 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 --
timestep 2.0
dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
# The following commands are useful if you want to calculate the distribution
# of alkane-chain radius-of-gyration at a given temperature & pressure.
#compute cRg TraPPE gyration
#variable vRg equal c_cRg
#compute cPE all pe
#variable vPE equal c_cPE
#fix FprintPE all print 1000 "${vPE}" file U.dat
#fix FprintRg all print 1000 "${vRg}" file Rg.dat
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 1000 # time interval for printing out "thermo" data
#thermo_modify flush yes
restart 100000 restart_nvt
run 1000000
write_data system_after_nvt.data
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