equi.in

units          lj
atom_style     full
boundary       p p f

### Force field ###
#                     r_cut
pair_style     lj/cut 2.5
pair_modify    shift yes
bond_style     fene
special_bonds  fene

read_data      ${initial_data}

#                K    R0  e   s
bond_coeff     1 30.0 1.5 1.0 1.0

# 'Static' pair coefficients
#                e     s   cutoff
pair_coeff * *   1.0   1.0 1.12446 # General repulsive
pair_coeff 3 3   1.0   1.0 2.5     # Solvent-solvent

# Dynamic pair coefficents
#                  e      s   cutoff
pair_coeff 1*2 1*2 ${epp} 1.0 2.5
pair_coeff 1*2 3   ${eps} 1.0 ${cps}

### Run settings ###
timestep       0.005
neighbor       0.8 bin
neigh_modify   delay 1 every 1 check yes

# Grafting layer
group          grafting type 1
group          mobile subtract all grafting
fix            walls all wall/harmonic zlo EDGE 100 1 1
fix            freezeGrafting grafting setforce 0 0 0
neigh_modify   exclude group grafting grafting

### Output ###
shell          mkdir img_equi
dump           1 all image 10000 img_equi/*.jpg type type view 90 90 size 1000 1000 zoom 2

# Initial velocity
compute        Tmobile mobile temp
velocity       mobile create ${T_RT} 5324324 temp Tmobile
thermo         1000
thermo_style   custom step temp pe etotal press c_Tmobile cpuremain

# Minimize
minimize       1E-8 1E-8 10000 10000

# Run with limit and frequent balance
fix            nveinit        mobile nve/limit 1
fix            lv             mobile langevin ${T_RT} ${T_RT} 1000 ${seed}
fix_modify     lv             temp Tmobile
fix            balance        mobile balance 10000 1.1 shift z 10 1.1 weight time 1

run            10000

minimize       1E-8 1E-8 10000 10000

unfix          nveinit
unfix          lv
fix            nve            mobile nve
fix            lv             mobile langevin ${T_RT} ${T_RT} 100 ${seed}
fix_modify     lv             temp Tmobile
run            200000

write_restart  restart.equi
write_data     data.equi