run.in.npt

# PREREQUISITES:
#
#      You must use moltemplate.sh (& packmol?) to create 3 files:
#        system.data  system.in.init  system.in.settings
#
# See "README_setup.sh" for instructions how to use moltemplate.sh
# Note: This input script file only covers equilibration of the system.
#
# ------------------------------- Initialization Section --------------------

include         "system.in.init"

# ------------------------------- Atom Definition Section -------------------

read_data       "system.data"

# ------------------------------- Settings Section --------------------------

include         "system.in.settings"

# ------------------------------- Run Section -------------------------------

# -- simulation protocol --

# (Groups "gElbaWater" and "gMethanol" are defined in "system.in.settings"
#  Rename them to "gSolvent" and "gSolute")
group gSolvent union gElbaWater gElbaWater
group gSolute union gMethanol gMethanol

# Randomize the direction of the solvent dipoles
set group gSolvent dipole/random 9876 0.541 

velocity all create 298.0 9876 

neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes

timestep 2.0

fix 1 gSolute nve # integrate gSolute
fix 2 gSolvent nve/sphere update dipole # integrate gSolvent
fix 3 gSolute langevin 298.0 298.0 1000 9876 # thermostat gSolute
fix 4 gSolvent langevin 298.0 298.0 1000 9876 omega yes zero yes # thermostat gSolvent
fix 5 all press/berendsen iso 1.0 1.0 1000 modulus 21740 # barostat
fix 6 all momentum 500 linear 1 1 1 
fix 7 gSolute rattle 1.0e-6 100 0 m 1.0

dump  1 all custom 1000 traj_nvt.lammpstrj id mol type x y z mux muy muz ix iy iz

thermo_style custom step temp etotal pe epair press
thermo_modify norm yes flush yes 
thermo 100

run 10000