# two monomer nylon example
# reaction produces a condensed water molecule

units real

boundary p p p

atom_style full

kspace_style pppm 1.0e-4

pair_style lj/class2/coul/long 8.5

angle_style class2

bond_style class2

dihedral_style class2

improper_style class2

special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower

read_data tiny_nylon.data &
  extra/bond/per/atom 5  &
  extra/angle/per/atom 15 &
  extra/dihedral/per/atom 15 &
  extra/improper/per/atom 25 &
  extra/special/per/atom 25

variable runsteps equal 1000
variable prob1 equal step/v_runsteps*2+0.1
variable prob2 equal (step/v_runsteps)>0.5

velocity all create 300.0 4928459 dist gaussian

molecule mol1 rxn1_stp1_unreacted.molecule_template
molecule mol2 rxn1_stp1_reacted.molecule_template
molecule mol3 rxn1_stp2_unreacted.molecule_template
molecule mol4 rxn1_stp2_reacted.molecule_template

thermo 50

# dump 1 all xyz 1 test_vis.xyz
# dump_modify 1 types labels

fix myrxns all bond/react stabilization yes statted_grp .03 &
  react rxn1 all 1 0.0 5.0 mol1 mol2 rxn1_stp1_map prob v_prob1 1234 &
  react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map prob v_prob2 1234 rescale_charges yes

fix 1 statted_grp_REACT nvt temp 300 300 100

# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1

thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*]

# restart 100 restart1 restart2

run ${runsteps}

# write_restart restart_longrun
# write_data restart_longrun.data