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#
# define units
#
units lj
#
# specify periodic boundary conditions
#
boundary p p p
#
# define atom_style
# full covers everything
#
atom_style full
#
# Read the restart file and restart the counter on timesteps
#
read_restart lj.equilibration.restart.100000
reset_timestep 0
#
# define mass
#
# mass of atom type 1
mass 1 1.0
mass 2 1.0
#
# specify interaction potential
# pairwise interaction via the Lennard-Jones potential with a cut-off at 2.5 lj-sigma
#
pair_style lj/cut 2.5
# specify parameters between atoms of type 1 with an atom of type 1
# epsilon = 1.0, sigma = 1.0, cutoff = 2.5
pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 2 2 1.2 0.9 2.5
#
# specify parameters for neighbor list
# rnbr = rcut + 0.3
#
neighbor 0.3 bin
#
# Specify timestep
#
timestep 0.001
#
# Write thermodynamic parameters to log
#
thermo_style custom step pe ke etotal temp press density
thermo 1000
thermo_modify norm no
#
# Setup plumed and that we are going to run npt equilibration
#
fix 1 all plumed plumedfile plumed.dat outfile p.log
fix 2 all nvt temp 1.0 1.0 0.1
#
# save trajectory and restart file
# dumpid = 1
# filename = output.xyz
#
dump 1 all xyz 1000 output.xyz
dump_modify 1 element Ar Ne
restart 100000 lj.prod.restart
#
# Run 5000000 of equilibration
#
run 100000