units real atom_style full bond_style harmonic angle_style harmonic dihedral_style harmonic improper_style umbrella special_bonds dreiding # Coefficients in non-bonding are just as an example pair_style lj/cut 15.0 #kspace_style ewald 0.0001 #kspace_modify gewald 1.0 #dielectric 1.0 read_data output.data extra/special/per/atom 10 extra/bond/per/atom 10 extra/angle/per/atom 10 extra/dihedral/per/atom 10 extra/improper/per/atom 10 #replicate 2 2 2 molecule pre prepy2.mol molecule post postpy2.mol thermo 500 #minimize 0.0 0.0 10000 100000 velocity all create 300 1666343046 mom yes rot yes dist gaussian #Basic Molecular Dynamics Run timestep 1.0 dump 1 all atom 500 dump.lammpstrj thermo_style custom step temp density fix 1 all npt temp 300 300 100.0 iso 1.0 1.0 1000.0 run 200000 unfix 1 fix fxrct all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 10.0 pre post automap.data stabilize_steps 100 fix 1 statted_grp_REACT nvt temp 400.0 400.0 100 fix 4 bond_react_MASTER_group temp/rescale 1 400.0 400.0 10 1 thermo_style custom step temp density f_fxrct[*] thermo 100 run 400000 write_data output*.data