input.lammps

# Bulk TIP4P/2005 water system with NaCl ions
# variables
variable pre equal 1 # desired pressure (Atm)
variable tem equal 293.15 # desired temperature (K)

# main parameters
units real # style of units (A, fs, Kcal/mol)
atom_style full # molecular + charge
bond_style harmonic
angle_style harmonic
boundary p p p # periodic boundary conditions
pair_style lj/cut/tip4p/long 1 2 1 1 0.1546 10 # cut-off 1 nm
kspace_style pppm/tip4p 1.0e-4
pair_modify mix arithmetic tail yes # eij = sqrt(ei*ej), dij = 0.5*(di+dj)

# import positions and parameters
read_data conf.data
include PARM.lammps

# groups # descriptions
group wat type 1 2 # bulk water
group nacl type 3 4 # na cl

# dynamics
velocity all create ${tem} 4928459 rot yes mom yes dist gaussian
timestep 2 # (fs)
fix myshk wat shake 1.0e-5 200 0 b 1 a 1 # shake with increased precision
fix mynpt all npt temp ${tem} ${tem} 100 iso ${pre} ${pre} 1000 # npt equilibrium

# output 
dump dp1 all atom 1000 dump.lammpstrj
thermo 1000 

# equilibration run 
run 50000 # 100 ps
write_data equilibrium.data

# production run 
run 1000000 # 2 ns