units real dimension 3 newton off processors * * * boundary p p p atom_style full ##force field pair_style lj/cut/coul/long 12.0 bond_style harmonic angle_style harmonic dihedral_style opls kspace_style pppm 1.0e-5 #region world block 0.00000 29.400 0.00000 29.400 0.00000 29.400 read_data ./water-spcemodel.data extra/bond/types 04 extra/atom/types 6 extra/dihedral/types 6 extra/angle/types 6 extra/special/per/atom 100 extra/bond/per/atom 10 extra/angle/per/atom 16 extra/dihedral/per/atom 36 molecule pentanol pentanol.txt offset 2 1 1 0 0 #import pentanol region void1 sphere 11.52 15.22 12.67 12.0 # create a spherical void region at x,y,z and r(radius) mass 1 15.999 #OW mass 2 1.008 #HW mass 3 12.011 #C mass 4 12.011 #C mass 5 1.008 #H mass 6 12.011 #C mass 7 15.999 #O mass 8 1.008 #H # Atom type1 type2 epsilon sigma Cutoff distance L-J pair_coeff 1 1 0.155 3.16 12.0 #O-spce pair_coeff 2 2 0.000 0.00 12.0 #H-spce pair_coeff 3 3 0.070 3.50 12.0 #C1 pair_coeff 4 4 0.070 3.50 12.0 #C2 pair_coeff 5 5 0.030 2.50 12.0 #HC pair_coeff 6 6 0.070 3.50 12.0 #C pair_coeff 7 7 0.170 3.12 12.0 #OH pair_coeff 8 8 0.000 0.00 12.0 #HO pair_modify mix arithmetic #used airthmatic combined rule for the cross term in L-J cross-pair #Bonds bond-type kb req bond_coeff 1 450.00 1.000 #Ow-HW bond_coeff 2 268.00 1.529 #C-C bond_coeff 3 340.00 1.09 #C-H bond_coeff 4 320.00 1.41 #C-H bond_coeff 5 553.00 0.945 #O-H #Angles Angle-type k equbm-angle Kub rub angle_coeff 1 55.00 109.47 angle_coeff 2 37.50 110.70 #CCH angle_coeff 3 33.00 107.80 #HCH angle_coeff 4 58.35 112.70 #CCC angle_coeff 5 50.00 109.5 #CCO angle_coeff 6 35.00 109.5 #HCO angle_coeff 7 55.00 108.5 #COH #Dihedrals Type K1 K2 K3 K4 (coefficients for the opls dihedral equation) dihedral_coeff 1 0.00 0.00 0.30 0.00 #HCCC dihedral_coeff 2 0.00 0.00 0.30 0.00 #HCCH dihedral_coeff 3 0.00 0.00 0.468 0.00 #HCCO dihedral_coeff 4 1.30 -0.050 0.20 0.00 #CCCC dihedral_coeff 5 -0.356 -0.174 0.492 0.00 #CCOH dihedral_coeff 6 0.00 0.00 0.352 0.00 #HCOH create_atoms 0 random 30 34534533453 void1 mol pentanol 5234765 group water type 1 2 group pent type 3 4 5 6 7 8 neighbor 1.0 bin neigh_modify delay 0 every 1 check yes thermo 200 min_style quickmin minimize .00001 .00001 100000 100000 # minimize the structure with the default conjugate-gradiet algorithm, default min_style is cg special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.8333 dihedral no fix 1 all nvt temp 300 300 300 write_dump water atom dump1.lammpstrj dump replay1 all custom 10 ./zeolitetest1.lammpstrj id type xu yu zu restart 10000 restart_zeolite timestep 0.5 fix 4 water shake 1.0e-4 20 1000 b 1 a 1 run 100000