units real dimension 3 newton off processors * * * boundary p p p atom_style full ##force field pair_style lj/cut/coul/long 15.0 #pair_style hybrid buck/coul/long 15.0 lj/cut/coul/long 15.0 #if you want multiple pair styles bond_style harmonic angle_style harmonic dihedral_style opls kspace_style pppm 1.0e-5 region world block 0.00000 25.264 0.00000 25.264 0.00000 26.186 read_data ./zeolite-glu.txt extra/bond/types 1 extra/atom/types 2 extra/dihedral/types 0 extra/angle/types 1 extra/special/per/atom 10 extra/bond/per/atom 2 extra/angle/per/atom 4 extra/dihedral/per/atom 6 molecule wtr watermolecule.txt offset 10 7 38 57 0 #import water #molecule glucose glucose.txt offset 4 1 1 0 0 #import glucose molecule region void1 sphere 12.68 10.27 13.15 4.0 # create a spherical void region region void2 sphere 22.68 10.27 13.15 4.0 # create a spherical void region mass 1 15.999 #O mass 2 28.0855 #Si mass 3 15.9994 mass 4 12.0110 mass 5 1.0080 mass 6 12.0110 mass 7 1.0080 mass 8 15.9994 mass 9 1.0080 mass 10 12.0110 mass 11 15.999400 #0 mass 12 1.0079401 #H pair_coeff 1 1 0.044 2.30 9.0 #Si-Si pair_coeff 2 2 0.152 3.15 9.0 #OW-OW TIP3p pair_coeff 3 3 0.000 0.00 9.0 #HW-HW TIP3P pair_coeff 4 4 0.210 2.96 9.0 #Aldehyde-O pair_coeff 5 5 0.105 3.75 9.0 #Ald-C pair_coeff 6 6 0.015 2.42 9.0 #H-Ald pair_coeff 7 7 0.066 3.50 9.0 #C-CH-CHOH pair_coeff 8 8 0.030 2.50 9.0 #H-alkanes pair_coeff 9 9 0.170 3.07 9.0 #O-diol pair_coeff 10 10 0.000 0.00 9.0 #H-diol pair_coeff 11 11 0.066 3.50 9.0 #C-CH2OH pair_coeff 12 12 0.105 3.30 9.0 #O-O pair_modify mix arithmetic #if using hybrid: #pair_coeff 1 1 buck/coul/long A 1/rho C #pair_coeff 1 3 lj/cut/coul/long A B #Bonds bond_coeff 1 320.00 1.2161 #C-O aldehyde-modify bond_coeff 2 340.00 1.1090 #C-H aldehyde-modify bond_coeff 3 268.00 1.5196 #CAld-CAlc(4)-modify bond_coeff 4 340.00 1.1095 #C4-H5 bond_coeff 5 320.00 1.4097 #C4-O6 bond_coeff 6 268.00 1.5504 #C4-C8 bond_coeff 7 553.00 0.9717 #O6-H7 bond_coeff 8 340.00 1.0923 #C8-H9 bond_coeff 9 320.00 1.4243 #C8-O10 bond_coeff 10 268.00 1.5631 #C8-C12 bond_coeff 11 553.00 0.9731 #O10-H11 bond_coeff 12 340.00 1.0949 #C12-H13 bond_coeff 13 320.00 1.4328 #C12-O14 bond_coeff 14 268.00 1.5427 #C12-C16 bond_coeff 15 553.00 0.9689 #O14-H15 bond_coeff 16 340.00 1.1004 #C16-H17 bond_coeff 17 320.00 1.4152 #C16-O18 bond_coeff 18 268.00 1.5289 #C16-C20 bond_coeff 19 553.00 0.9713 #O18-H19 bond_coeff 20 340.00 1.1031 #C20-H21 bond_coeff 21 340.00 1.1089 #C20-H22 bond_coeff 22 320.00 1.4180 #C20-O23 bond_coeff 23 553.00 0.9650 #O23-H24 bond_coeff 24 450.00 0.9572 #OW-HW #Angles angle_coeff 1 35.00 121.36 #O1-C2-H3 Aldehyde angle-modify angle_coeff 2 50.00 124.86 #O1-C2-C4-modify angle_coeff 3 37.50 113.76 #H3-C2-C4-modify angle_coeff 4 37.50 106.55 #C2-C4-H5-modify angle_coeff 5 50.0 106.88 #C2-C4-O6-modify angle_coeff 6 58.35 113.36 #C2-C4-C8 angle_coeff 7 35.00 111.04 #H5-C4-O6 angle_coeff 8 37.50 107.97 #H5-C4-C8 angle_coeff 9 50.00 110.97 #O6-C4-C8 angle_coeff 10 55.00 104.85 #C4-O6-H7 angle_coeff 11 37.50 108.85 #C4-C8-H9 angle_coeff 12 50.00 107.89 #C4-C8-O10 angle_coeff 13 58.35 112.38 #C4-C8-C12 angle_coeff 14 35.00 106.63 #H9-C8-O10 angle_coeff 15 37.50 109.84 #H9-C8-C12 angle_coeff 16 50.00 111.05 #O10-C8-C12 angle_coeff 17 55.00 105.20 #C8-O10-H11 angle_coeff 18 37.50 108.84 #C8-C12-H13 angle_coeff 19 50.00 110.25 #C8-C12-O14 angle_coeff 20 58.35 112.37 #C8-C12-C16 angle_coeff 21 35.00 104.64 #H13-C12-O14 angle_coeff 22 37.50 108.25 #H13-C12-C16 angle_coeff 23 50.00 112.13 #O14-C12-C16 angle_coeff 24 55.00 107.28 #C12-O14-H15 angle_coeff 25 37.50 108.69 #C12-C16-H17 angle_coeff 26 50.00 110.99 #C12-C16-O18 angle_coeff 27 58.35 111.19 #C12-C16-C20 angle_coeff 28 35.00 105.50 #H17-C16-O18 angle_coeff 29 37.50 107.67 #H17-C16-C20 angle_coeff 30 50.00 112.52 #O18-C16-C20 angle_coeff 31 55.00 108.04 #C16-O18-H19 angle_coeff 32 37.50 108.31 #C16-C20-H21 angle_coeff 33 37.50 109.07 #C16-C20-H22 angle_coeff 34 50.00 108.13 #C16-C20-O23 angle_coeff 35 33.00 107.54 #H21-C20-H22 angle_coeff 36 35.00 111.91 #H21-C20-O23 angle_coeff 37 35.00 111.80 #H22-C20-O23 angle_coeff 38 55.00 108.08 #C20-O23-H24 angle_coeff 39 55.00 104.52 #water tip3p model #Dihedrals dihedral_coeff 1 0.00 0.00 0.4668 0.00 # -77.00 O1-C2-C4-H5-modify (1-7) dihedral_coeff 2 9.066 0.00 0.000 0.00 # 163.95 O1-C2-C4-O6 dihedral_coeff 3 -1.336 0.0 0.0 0.00 # 41.38 O1-C2-C4-C8 dihedral_coeff 4 0.0 0.0 0.318 0.00 # 102.20 H3-C2-C4-H5 dihedral_coeff 5 0.0 0.0 0.468 0.00 # -16.60 H3-C2-C4-O6 dihedral_coeff 6 0.0 0.0 0.366 0.00 # -139.18 H3-C2-C4-C8 dihedral_coeff 7 2.674 -2.883 1.026 0.00 # -157.35 C2-C4-O6-H7-modify uptohere dihedral_coeff 8 0.00 0.00 0.450 0.00 # 86.81 H5-C4-O6-H7 dihedral_coeff 9 2.674 -2.883 1.026 0.00 # -33.29 C8-C4-O6-H7 dihedral_coeff 10 0.00 0.00 0.3666 0.00 # 48.54 C2-C4-C8-H9 dihedral_coeff 11 -1.336 0.0 0.0 0.00 # 163.88 C2-C4-C8-O10 dihedral_coeff 12 1.74 -0.157 0.279 0.00 # -73.36 C2-C4-C8-C12 dihedral_coeff 13 0.0 0.0 0.318 0.00 # 166.35 H5-C4-C8-H9 dihedral_coeff 14 0.0 0.0 0.468 0.00 # -78.31 H5-C4-C8-O10 dihedral_coeff 15 0.0 0.0 0.318 0.00 # 44.45 H5-C4-C8-C12 dihedral_coeff 16 0.0 0.0 0.468 0.00 # -71.74 O6-C4-C8-H9 dihedral_coeff 17 9.066 0.0 0.0 0.00 # 43.60 O6-C4-C8-O10 dihedral_coeff 18 -1.336 0.0 0.0 0.00 # 166.36 O6-C4-C8-C12 dihedral_coeff 19 2.674 -2.883 1.026 0.00 # 86.72 C4-C8-O10-H11 dihedral_coeff 20 0.00 0.00 0.450 0.00 # -156.49 H9-C8-O10-H11 dihedral_coeff 21 2.674 -2.883 1.026 0.00 # -36.85 C12-C8-O10-H11 dihedral_coeff 22 0.0 0.0 0.366 0.00 # 8.86 C4-C8-C12-H13 dihedral_coeff 23 -1.336 0.0 0.0 0.00 # -105.37 C4-C8-C12-O14 dihedral_coeff 24 1.74 -0.157 0.279 0.00 # -128.75 C4-C8-C12-C16 dihedral_coeff 25 0.0 0.0 0.318 0.00 # -112.47 H9-C8-C12-H13 dihedral_coeff 26 0.0 0.0 0.468 0.00 # 133.30 H9-C8-C12-O14 dihedral_coeff 27 0.0 0.0 0.366 0.00 # 7.41 H9-C8-C12-C16 dihedral_coeff 28 0.0 0.0 0.468 0.00 # 129.83 O10-C8-C12-H13 dihedral_coeff 29 9.066 0.0 0.0 0.00 # 15.59 O10-C8-C12-O14 dihedral_coeff 30 -1.336 0.0 0.0 0.00 # -110.29 O10-C8-C12-C16 dihedral_coeff 31 2.674 -2.883 1.026 0.00 # -81.09 C8-C12-O14-H15 dihedral_coeff 32 0.0 0.0 0.450 0.00 # 162.03 H13-C12-O14-H15 dihedral_coeff 33 2.674 -2.883 1.026 0.00 # 44.93 C16-C12-O14-H15 dihedral_coeff 34 0.0 0.0 0.366 0.00 # 68.20 C8-C12-C16-H17 dihedral_coeff 35 -1.336 0.0 0.0 0.00 # -47.38 C8-C12-C16-O18 dihedral_coeff 36 1.74 -0.157 0.279 0.00 # -173.45 C8-C12-C16-C20 dihedral_coeff 37 0.0 0.0 0.366 0.00 # -171.57 C13-C12-C16-H17 dihedral_coeff 38 -1.336 0.0 0.0 0.00 # 72.84 C13-C12-C16-O18 dihedral_coeff 39 0.0 0.0 0.366 0.00 # -53.23 H13-C12-C16-C20 dihedral_coeff 40 0.0 0.0 0.468 0.00 # -56.65 O14-C12-C16-H17 dihedral_coeff 41 9.066 0.0 0.0 0.00 # -172.24 O14-C12-C16-O18 dihedral_coeff 42 -1.336 0.0 0.0 0.00 # 61.69 O14-C12-C16-C20 dihedral_coeff 43 2.674 -2.883 1.026 0.00 # -49.38 C12-C16-O18-H19 dihedral_coeff 44 0.0 0.0 0.450 0.00 # -166.93 H17-C16-O18-H19 dihedral_coeff 45 2.674 -2.883 1.026 0.00 # 75.94 C20-C16-O18-H19 dihedral_coeff 46 0.0 0.0 0.366 0.00 # 72.61 C12-C16-C20-H21 dihedral_coeff 47 0.0 0.0 0.366 0.00 # -44.15 C12-C16-C20-H22 dihedral_coeff 48 -1.336 0.0 0.0 0.00 # -165.93 C12-C16-C20-O23 dihedral_coeff 49 0.0 0.0 0.318 0.00 # -168.43 H17-C16-C20-H21 dihedral_coeff 50 0.0 0.0 0.318 0.00 # 74.81 H17-C16-C20-H22 dihedral_coeff 51 0.0 0.0 0.468 0.00 # -46.98 H17-C16-C20-O23 dihedral_coeff 52 0.0 0.0 0.468 0.00 # -52.60 O18-C16-C20-H21 dihedral_coeff 53 0.0 0.0 0.468 0.00 # -169.36 O18-C16-C20-H22 dihedral_coeff 54 9.066 0.0 0.0 0.00 # 68.86 O18-C16-C20-O23 dihedral_coeff 55 2.674 -2.883 1.026 0.00 # -174.31 C16-C20-O23-H24 dihedral_coeff 56 0.0 0.0 0.450 0.00 # -55.11 H21-C20-O23-H24 dihedral_coeff 57 0.0 0.0 0.450 0.00 # 65.61 H22-C20-O23-H24 group Si type 2 group O type 1 group zeolite union Si O fix 2 zeolite setforce 0 0 0 set type 1 charge -0.75 #set the charge on all atoms of type 1 set type 2 charge 1.50 #create_atoms 0 random 10 523452422 void mol wtr 5234765 #create 10 water atoms in the region void create_atoms 0 random 20 34534533453 void1 mol wtr 5234765 #Need to corrected #create_atoms 0 random 20 34534533453 void2 mol wtr 5234765 #Need to corrected neighbor 1.0 bin neigh_modify delay 0 every 1 check yes thermo 200 minimize .00001 .00001 100000 100000 fix 1 all nvt temp 300 300 300 restart 1000 restart_zeolite dump replay all atom 1 ./zeolitetest.lammpstrj timestep .5 fix 3 all viscous .8 run 10000 unfix 3