# 3d Lennard-Jones h20 # Comments from manual, see pag 35 # 1. Initialization: processors 2 2 2 units real boundary p p p dimension 3 atom_style full neighbor 2.0 bin neigh_modify every 1 delay 0 check yes page 300000 one 5000 # 2. Atom definition: read_data 120ch3cooh.lammps05 mass 1 12.011 # C (-H) mass 2 12.011 # C (-C) mass 3 15.9994 # O (=O) mass 4 15.9994 # O (-H) mass 5 1.008 # H (C-H) mass 6 1.008 # H (O-H) mass 7 15.999400 mass 8 1.008 mass 9 1.0e-6 group acetic type 1 2 3 4 5 6 group water type 7 8 9 timestep 0.1 # 3. Force fields: pair_style lj/cut/coul/long 14.0 # I J eps(kcal/mol) sigma(A) pair_coeff 1 1 0.066 3.5 #C(CH) pair_coeff 1 2 0.0832 3.625 pair_coeff 1 3 0.1177 3.23 pair_coeff 1 4 0.1059 3.25 pair_coeff 1 5 0.0445 3.0 pair_coeff 1 6 0 0 pair_coeff 1 7 0.1027 3.31 pair_coeff 1 8 0 0 pair_coeff 1 9 0 0 pair_coeff 2 2 0.105 3.75 #C(C=O) pair_coeff 2 3 0.1485 3.355 pair_coeff 2 4 0.1336 3.375 pair_coeff 2 5 0.0561 3.125 pair_coeff 2 6 0 0 pair_coeff 2 7 0.1296 3.435 pair_coeff 2 8 0 0 pair_coeff 2 9 0 0 pair_coeff 3 3 0.21 2.96 #O(=O) pair_coeff 3 4 0.1889 2.98 pair_coeff 3 5 0.0794 2.73 pair_coeff 3 6 0 0 pair_coeff 3 7 0.1832 3.04 pair_coeff 3 8 0 0 pair_coeff 3 9 0 0 pair_coeff 4 4 0.17 3.0 #O(OH) pair_coeff 4 5 0.0714 2.75 pair_coeff 4 6 0 0 pair_coeff 4 7 0.1649 3.06 pair_coeff 4 8 0 0 pair_coeff 4 9 0 0 pair_coeff 5 5 0.03 2.5 #H(CH) pair_coeff 5 6 0 0 pair_coeff 5 7 0.0693 2.81 pair_coeff 5 8 0 0 pair_coeff 5 9 0 0 pair_coeff 6 6 0 0 #H(OH) pair_coeff 6 7 0 0 pair_coeff 6 8 0 0 pair_coeff 6 9 0 0 pair_coeff 7 7 0.1599 3.12 #O-O pair_coeff 7 8 0 0 pair_coeff 7 9 0 0 pair_coeff 8 8 0 0 #H-H pair_coeff 8 9 0 0 pair_coeff 9 9 0 0 bond_style harmonic # N k/2(kcal/mol/A^2) r0(A) bond_coeff 1 340 1.09 #c-h bond_coeff 2 317 1.522 #c-c bond_coeff 3 570 1.229 #c=o bond_coeff 4 450 1.364 #c-o bond_coeff 5 553 0.945 #o-h angle_style harmonic # N k/2(kcal/mol/rad^2) theta0(degree) K_UB(en/dis^2) rub(A) angle_coeff 1 33 107.8 #H-C-H angle_coeff 2 35 109.5 #H-C-C angle_coeff 3 80 120.4 #C-C=O angle_coeff 4 70 108 #C-C-O angle_coeff 5 80 121 #O=C-O angle_coeff 6 35 113 #C-O-H dihedral_style opls # N K1(kcal/mol) K2 K3 K4 dihedral_coeff 1 0 0 0 0 #H-C-C=O dihedral_coeff 2 0 0 0 0 #H-C-C-O dihedral_coeff 3 1.5 5.5 0 0 #C-C-O-H dihedral_coeff 4 0 5.5 0 0 #O=C-O-H kspace_style pppm 1.0e-4 variable T equal 100 velocity all create 100 87287 loop all dist gaussian fix a1 acetic nvt temp $T $T 100 fix b1 water rigid/nvt molecule temp $T $T 100 compute t1 acetic temp compute t2 water temp dump 1 all custom 5000 dump.meltq401 id type x y z mass q thermo_style custom step temp c_t1 c_t2 thermo 500 run 5000000 write_data data.120acetic4ns