#try out input file, without couloumbic, martini lj units real dimension 3 #processors 2 1 1 grid onelevel map cart boundary p p p atom_style angle pair_style lj/gromacs 9.0 12.0 bond_style harmonic angle_style cosine/squared read_data input.data #the unit of energy here is kcal. #the unit of distance is angston pair_coeff 1 1 1.33 4.7 pair_coeff 1 2 1.33 4.7 pair_coeff 1 3 1.19 4.7 pair_coeff 1 4 1.33 4.7 pair_coeff 1 5 1.33 4.7 pair_coeff 1 6 1.0 4.7 pair_coeff 2 2 1.33 4.7 pair_coeff 2 3 1.19 4.7 pair_coeff 2 4 1.33 4.7 pair_coeff 2 5 1.33 4.7 pair_coeff 2 6 1.0 4.7 pair_coeff 3 3 0.95 4.7 pair_coeff 3 4 1.19 4.7 pair_coeff 3 5 1.19 4.7 pair_coeff 3 6 1.0 4.7 pair_coeff 4 4 1.33 4.7 pair_coeff 4 5 1.33 4.7 pair_coeff 4 6 1.0 4.7 pair_coeff 5 5 1.19 4.7 pair_coeff 5 6 1.0 4.7 pair_coeff 6 6 1.19 4.7 #take care of coeff unit mass * 72 bond_coeff * 1.000 4.7 angle_coeff * 0 120 #special bond for weighting factors of special_bonds fene timestep 20 neighbor 2.0 bin neigh_modify delay 10 binsize 2.0 fix damp all npt temp 310.0 310.0 2000.0 iso 3.0 2.0 2000.0 group geletin type 1 2 3 4 5 group water type 6 group all type 1 2 3 4 5 6 dump distribution geletin xyz 1000 distri.xyz dump solvent water xyz 1000 water.xyz dump_modify distribution element O N C S P H thermo 10000 restart 50000 knot run 100000