# Use the OPLS-AA force field for all species.
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
import PolyNIPAM.lt

# Define the SPC water and ions as in the OPLS-AA
Ca inherits OPLSAA {
  write("Data Atoms"){
    $atom:a1  $mol:. @atom:412 0.0  0.00000 0.00000 0.000000
  }
}

Cl inherits OPLSAA {
  write("Data Atoms"){
    $atom:a1  $mol:. @atom:401 0.0  0.00000 0.00000 0.000000
  }
}

SPC inherits OPLSAA {
  write("Data Atoms"){
    $atom:O  $mol:. @atom:9991 0.  0.0000000 0.00000 0.000000
    $atom:H1 $mol:. @atom:9990 0.  0.8164904 0.00000 0.5773590
    $atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
  }
  write("Data Bond List") {
    $bond:OH1 $atom:O $atom:H1
    $bond:OH2 $atom:O $atom:H2
  }
}

# Create the sample.
wat=new SPC[500]
pol=new PolyNIPAM[1]
cat=new Ca[1]
ani=new Cl[2]

# Periodic boundary conditions:
write_once("Data Boundary"){
  0 26 xlo xhi
  0 26 ylo yhi
  0 26 zlo zhi
}

write_once("In Init"){
  boundary p p p  # "p p p" is the default. This line is optional.
  neighbor 3 bin  # (This line is also optional in this example.)
}

# Note: The lines below in the "In Run" section are often omitted.

# Run an NVT simulation.
write_once("In Run"){
  # Input variables.
  variable run    string sample01  # output name
  variable ts     equal  2         # timestep
  variable temp   equal  298.15    # equilibrium temperature
  variable p      equal  1.        # equilibrium pressure
  variable equi   equal  30000     # equilibration steps

  # Set the output.
  thermo          1000
  thermo_style    custom step etotal evdwl ecoul elong ebond eangle &
  edihed eimp pe ke temp press atoms vol density cpu
  thermo_modify flush yes
  compute pe1 all pe/atom pair
  dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1

  # Minimise the input structure, just in case.
  minimize        .01 .001 1000 100000
  write_data \$\{run\}.min

  # Set the constrains.
  group watergroup type @atom:9991 @atom:9990
  fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH

  # Short annealing.
  timestep        \$\{ts\}
  fix       1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
  velocity    all create \$\{temp\} 315443
  run             \$\{equi\}
  unfix 1
}