run.in

units         lj
atom_style    full
dimension     3
boundary      p p p
neighbor      1.0 bin
neigh_modify  one 8000 every 1
kspace_style  pppm 1.0e-4
dielectric    1.0

# data file with coacervate slab in the center of the box, crowders and salt on either side
read_data     start.data 

bond_style    fene
bond_coeff    * 30.0 1.5 1.0 1.0
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0

set           type 1 charge 1.0
set           type 3 charge 1.0
set           type 2 charge -1.0
set           type 4 charge -1.0

pair_style    lj/cut/coul/long 1.12 8.0
pair_coeff    * * 0.2 1.0
pair_coeff    * 5 0.2 1.0 1.12

variable      Temp equal 1.0
variable      Press equal 0.0
variable      dt equal 0.01
variable      Tdamping equal 100*${dt}
variable      velSeed equal 987457

thermo        1000
thermo_style  custom step temp ebond epair ke etotal enthalpy vol press spcpu
restart       1000000 restart
restart       10000 restart1 restart2

velocity      all create ${Temp} ${velSeed}
timestep      ${dt}


group         poly type 1 2
fix           freeze poly setforce 0.0 0.0 0.0
minimize      1.0e-4  1.0e-6  1000 10000
unfix         freeze


fix           nvtanneal all nvt temp 0.8  1.0 ${Tdamping}
fix           stabilize all momentum 5 linear 1 1 1
run           10000
unfix         nvtanneal
reset_timestep 0

dump          1 all custom 5000 traj.* id type xu yu zu  vx vy vz
fix           stabilize all momentum 5 linear 1 1 1
fix           nvt1 all nvt temp ${Temp} ${Temp} ${Tdamping}
run           25000

balance       0.9 shift y 20 1.0
fix           bal all balance 500000 0.9 shift y 20 1.0

run           10000000
write_data    final.data nocoeff nofix