Hi all Dear
i should simulated water for my project but my problem is hydrogen bonds in my data file and input files
HOW to create hbonds in my project ?
my data file :
84 atoms
56 bonds
28 angles
2 atom types
1 bond types
1 angle types
0.053 9.377 xlo xhi
0.196 9.953 ylo yhi
0.196 9.998 zlo zhi
Masses
1 1.008
2 15.9994
Pair Coeffs
1 0.046 0.4000135
2 0.1521 3.150574
Atoms
1 1 2 -0.834 2.75 8.844 9.629
2 1 1 0.417 2.11 8.29 9.998
3 1 1 0.417 2.164 9.245 8.962
4 2 2 -0.834 1.661 6.681 1.943
5 2 1 0.417 1.943 5.739 1.981
6 2 1 0.417 0.778 6.599 1.483
7 3 2 -0.834 4.618 8.125 7.777
8 3 1 0.417 5.405 7.919 8.314
9 3 1 0.417 4.002 8.458 8.422
10 4 2 -0.834 3.403 4.687 9.815
11 4 1 0.417 3.109 5.272 9.097
12 4 1 0.417 3.817 3.973 9.327
13 5 2 -0.834 2.71 6.185 7.54
14 5 1 0.417 2.467 6.236 6.561
15 5 1 0.417 3.41 6.855 7.58
16 6 2 -0.834 3.32 1.439 3.693
17 6 1 0.417 3.018 1.263 2.795
18 6 1 0.417 4.218 1.737 3.533
19 7 2 -0.834 4.539 2.605 8.295
20 7 1 0.417 5.46 2.702 8.123
21 7 1 0.417 4.434 1.616 8.363
22 8 2 -0.834 4.654 5.717 5.023
23 8 1 0.417 5.059 5.126 4.395
24 8 1 0.417 5.409 5.785 5.634
25 9 2 -0.834 3.686 8.353 3.401
26 9 1 0.417 4.494 7.93 3.084
27 9 1 0.417 3.041 7.727 3.197
28 10 2 -0.834 5.45 9.067 5.337
29 10 1 0.417 4.722 8.84 4.711
30 10 1 0.417 4.939 8.77 6.117
31 11 2 -0.834 2.421 3.775 5.058
32 11 1 0.417 2.684 2.934 4.652
33 11 1 0.417 3.219 4.34 5.048
34 12 2 -0.834 5.141 1.611 0.499
35 12 1 0.417 4.697 1.11 1.234
36 12 1 0.417 6.031 1.302 0.586
37 13 2 -0.834 5.461 6.754 1.943
38 13 1 0.417 6.412 6.627 2.018
39 13 1 0.417 5.209 5.956 1.434
40 14 2 -0.834 7.314 0.228 9.152
41 14 1 0.417 7.447 0.196 8.157
42 14 1 0.417 8.219 0.336 9.426
43 15 2 -0.834 7.529 4.508 1.396
44 15 1 0.417 8.313 4.582 0.857
45 15 1 0.417 6.783 4.511 0.768
46 16 2 -0.834 7.881 3.518 5.7
47 16 1 0.417 8.55 4.225 5.812
48 16 1 0.417 7.07 3.834 6.169
49 17 2 -0.834 9.016 4.086 8.814
50 17 1 0.417 9.377 5.001 8.813
51 17 1 0.417 8.726 3.741 9.661
52 18 2 -0.834 6.439 5.144 7.455
53 18 1 0.417 7.31 4.836 7.837
54 18 1 0.417 6.121 5.819 8.116
55 19 2 -0.834 6.255 9.802 0.364
56 19 1 0.417 6.954 9.121 0.671
57 19 1 0.417 5.459 9.264 0.196
58 20 2 -0.834 6.14 3.669 3.704
59 20 1 0.417 6.732 3.837 2.949
60 20 1 0.417 6.807 3.408 4.378
61 21 2 -0.834 0.688 2.781 7.114
62 21 1 0.417 1.488 3.19 6.703
63 21 1 0.417 0.053 3.429 6.93
64 22 2 -0.834 0.449 7.366 9.14
65 22 1 0.417 0.202 6.479 9.095
66 22 1 0.417 0.796 7.563 8.256
67 23 2 -0.834 2.278 3.922 1.2
68 23 1 0.417 2.701 3.392 0.56
69 23 1 0.417 1.556 3.406 1.415
70 24 2 -0.834 3.438 8.099 0.316
71 24 1 0.417 2.547 7.847 0.577
72 24 1 0.417 3.889 7.775 1.093
73 25 2 -0.834 1.314 9.385 7.173
74 25 1 0.417 1.333 8.706 6.444
75 25 1 0.417 2.056 9.953 6.98
76 26 2 -0.834 7.572 0.42 3.478
77 26 1 0.417 7.636 0.339 2.503
78 26 1 0.417 6.628 0.234 3.53
79 27 2 -0.834 1.133 7.08 5.078
80 27 1 0.417 1.201 7.102 4.137
81 27 1 0.417 0.358 6.549 5.302
82 28 2 -0.834 8.578 0.832 6.351
83 28 1 0.417 7.928 0.53 5.693
84 28 1 0.417 8.563 1.801 6.335
Bond Coeffs
1 450 0.9572
Bonds
1 1 1 2
2 1 1 3
3 1 4 5
4 1 4 6
5 1 7 8
6 1 7 9
7 1 10 11
8 1 10 12
9 1 13 14
10 1 13 15
11 1 16 17
12 1 16 18
13 1 19 20
14 1 19 21
15 1 22 23
16 1 22 24
17 1 25 26
18 1 25 27
19 1 28 29
20 1 28 30
21 1 31 32
22 1 31 33
23 1 34 35
24 1 34 36
25 1 37 38
26 1 37 39
27 1 40 41
28 1 40 42
29 1 43 44
30 1 43 45
31 1 46 47
32 1 46 48
33 1 49 50
34 1 49 51
35 1 52 53
36 1 52 54
37 1 55 56
38 1 55 57
39 1 58 59
40 1 58 60
41 1 61 62
42 1 61 63
43 1 64 65
44 1 64 66
45 1 67 68
46 1 67 69
47 1 70 71
48 1 70 72
49 1 73 74
50 1 73 75
51 1 76 77
52 1 76 78
53 1 79 80
54 1 79 81
55 1 82 83
56 1 82 84
Angle Coeffs
1 55 104.52
Angles
1 1 2 1 3
2 1 5 4 6
3 1 8 7 9
4 1 11 10 12
5 1 14 13 15
6 1 17 16 18
7 1 20 19 21
8 1 23 22 24
9 1 26 25 27
10 1 29 28 30
11 1 32 31 33
12 1 35 34 36
13 1 38 37 39
14 1 41 40 42
15 1 44 43 45
16 1 47 46 48
17 1 50 49 51
18 1 53 52 54
19 1 56 55 57
20 1 59 58 60
21 1 62 61 63
22 1 65 64 66
23 1 68 67 69
24 1 71 70 72
25 1 74 73 75
26 1 77 76 78
my input files :
units real
neigh_modify delay 2 every 1
atom_style full
bond_style harmonic
angle_style harmonic
pair_style lj/charmm/coul/long 8 10
pair_modify mix arithmetic
kspace_style pppm 1e-4
read_data solvate.data
minimize 0.001 0.001 1000 1000
fix 1 all nve
velocity all create 300.0 545 dist uniform
thermo 1
thermo_style multi
timestep 1
dump 1 all dcd 10 solvate.dcd
dump_modify 1 unwrap yes
run 2000