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小木虫论坛-学术科研互动平台 » 计算模拟区 » 分子模拟 » 其他 » data文件导入到VMD显示问题
北京石油化工学院2026年研究生招生接收调剂公告
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乔治大人

新虫 (初入文坛)

[求助] data文件导入到VMD显示问题

各位虫友好！

我在将水分子的数据文件导入VMD查看时，发现H原子的数量和位置异常，出现在键的夹角上。（如下图所示）想请教各位该如何解决？多谢指教！

附上数据文件：

LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.4 on Tue Aug 05 00:34:49 EDT 2014
192 atoms
128 bonds
64 angles
0 dihedrals
0 impropers
2 atom types
1 bond types
1 angle types
0 dihedral types
0 improper types
-0.025952 12.398448  xlo xhi
-0.072222 12.352178  ylo yhi
0.103767 12.528167  zlo zhi

Masses

1 15.999400 # O
2 1.008000 # H

Atoms # full

1 1 1 -1.112800 11.904200 11.004000 2.647150 # O
2 1 2 0.556400 11.274600 10.441300 3.165040 # H
3 1 2 0.556400 12.657229 10.697500 2.992120 # H
4 2 1 -1.112800 11.419600 1.182280 9.137010 # O
5 2 2 0.556400 11.398800 1.594150 8.310830 # H
6 2 2 0.556400 10.506300 0.898235 9.233160 # H
7 3 1 -1.112800 4.826680 1.783510 11.516400 # O
8 3 2 0.556400 4.546870 1.811150 10.564300 # H
9 3 2 0.556400 4.055660 1.238270 11.973500 # H
10 4 1 -1.112800 12.288000 1.904120 1.044200 # O
11 4 2 0.556400 11.828600 1.153600 0.839629 # H
12 4 2 0.556400 12.277700 2.333890 0.302505 # H
13 5 1 -1.112800 11.857500 1.676770 6.187920 # O
14 5 2 0.556400 11.648400 2.074730 5.284650 # H
15 5 2 0.556400 11.876700 0.812108 5.948150 # H
16 6 1 -1.112800 2.097890 5.057070 3.011100 # O
17 6 2 0.556400 2.136570 4.204340 2.822200 # H
18 6 2 0.556400 1.248920 5.503130 3.095170 # H
19 7 1 -1.112800 8.969570 9.662130 12.397100 # O
20 7 2 0.556400 9.686170 10.151600 12.437590 # H
21 7 2 0.556400 9.532380 8.853020 12.470100 # H
22 8 1 -1.112800 7.003800 0.166948 11.866400 # O
23 8 2 0.556400 7.602080 -0.008490 11.078100 # H
24 8 2 0.556400 6.314920 0.854812 11.845400 # H
25 9 1 -1.112800 7.279490 7.009030 4.039650 # O
26 9 2 0.556400 6.480970 6.584280 4.507850 # H
27 9 2 0.556400 7.966830 6.725300 4.670490 # H
28 10 1 -1.112800 4.968300 6.252330 2.294100 # O
29 10 2 0.556400 4.323490 6.517690 2.931870 # H
30 10 2 0.556400 5.091090 6.970190 1.641050 # H
31 11 1 -1.112800 9.233370 1.170670 1.198800 # O
32 11 2 0.556400 8.772080 2.002300 1.423460 # H
33 11 2 0.556400 8.648900 0.665205 0.687128 # H
34 12 1 -1.112800 10.128900 4.638490 3.506180 # O
35 12 2 0.556400 9.350580 4.298580 3.037750 # H
36 12 2 0.556400 9.946100 4.618830 4.531850 # H
37 13 1 -1.112800 2.868470 0.334175 0.677477 # O
38 13 2 0.556400 2.403840 0.200999 -0.138964 # H
39 13 2 0.556400 2.069790 0.770509 1.118620 # H
40 14 1 -1.112800 0.990607 8.880780 7.919540 # O
41 14 2 0.556400 1.468800 8.257450 8.474370 # H
42 14 2 0.556400 1.548730 9.628320 7.837180 # H
43 15 1 -1.112800 6.037680 11.965300 1.967580 # O
44 15 2 0.556400 6.711200 11.358900 2.192700 # H
45 15 2 0.556400 6.440020 12.350600 1.125540 # H
46 16 1 -1.112800 10.081700 7.285330 11.995600 # O
47 16 2 0.556400 9.502260 6.951850 12.805980 # H
48 16 2 0.556400 9.656250 6.986780 11.119000 # H
49 17 1 -1.112800 8.035030 3.368010 1.956490 # O
50 17 2 0.556400 7.178750 3.084810 2.288990 # H
51 17 2 0.556400 7.710830 4.079910 1.281810 # H
52 18 1 -1.112800 6.425050 9.669080 5.164110 # O
53 18 2 0.556400 5.437580 9.502120 5.160280 # H
54 18 2 0.556400 6.816230 9.186900 4.533480 # H
55 19 1 -1.112800 5.379420 6.514400 8.405390 # O
56 19 2 0.556400 5.755950 6.334530 9.297210 # H
57 19 2 0.556400 5.440740 7.514240 8.532830 # H
58 20 1 -1.112800 2.046140 1.943010 5.846200 # O
59 20 2 0.556400 1.143970 1.913690 6.058140 # H
60 20 2 0.556400 2.248230 1.154690 5.418870 # H
61 21 1 -1.112800 5.107140 1.201150 4.136430 # O
62 21 2 0.556400 5.044840 2.013910 3.551730 # H
63 21 2 0.556400 5.377520 0.578867 3.455080 # H
64 22 1 -1.112800 4.596620 8.523380 10.800400 # O
65 22 2 0.556400 5.239180 8.321920 11.448900 # H
66 22 2 0.556400 3.811110 8.904250 11.215900 # H
67 23 1 -1.112800 11.753800 2.360940 3.561900 # O
68 23 2 0.556400 11.219800 3.198640 3.682850 # H
69 23 2 0.556400 11.740900 2.309440 2.589890 # H
70 24 1 -1.112800 10.148400 9.230600 4.794850 # O
71 24 2 0.556400 10.724900 8.587640 4.193460 # H
72 24 2 0.556400 9.774880 8.755770 5.473800 # H
73 25 1 -1.112800 3.678800 8.862530 5.475880 # O
74 25 2 0.556400 3.654050 7.908400 5.269890 # H
75 25 2 0.556400 3.784180 9.231390 6.370230 # H
76 26 1 -1.112800 2.424500 5.061670 0.010513 # O
77 26 2 0.556400 2.259390 5.063060 1.073770 # H
78 26 2 0.556400 1.699730 5.358760 -0.532400 # H
79 27 1 -1.112800 2.031790 9.273860 3.335100 # O
80 27 2 0.556400 2.576050 9.625000 2.421210 # H
81 27 2 0.556400 2.552020 9.204230 4.251920 # H
82 28 1 -1.112800 0.671121 5.562010 10.459300 # O
83 28 2 0.556400 0.240613 4.699610 10.429400 # H
84 28 2 0.556400 1.201350 5.761520 9.675160 # H
85 29 1 -1.112800 2.186950 2.475840 2.653370 # O
86 29 2 0.556400 2.318520 2.024870 3.544650 # H
87 29 2 0.556400 1.317700 2.072840 2.368920 # H
88 30 1 -1.112800 2.189580 6.283080 8.069060 # O
89 30 2 0.556400 1.900250 6.315140 7.216860 # H
90 30 2 0.556400 3.129850 6.506460 8.013540 # H
91 31 1 -1.112800 8.673330 10.156400 9.670670 # O
92 31 2 0.556400 8.580570 10.190500 10.546700 # H
93 31 2 0.556400 9.689670 10.206300 9.469020 # H
94 32 1 -1.112800 3.925400 3.636840 7.691570 # O
95 32 2 0.556400 4.254210 4.458460 7.545880 # H
96 32 2 0.556400 2.917900 3.558790 7.218470 # H
97 33 1 -1.112800 2.091950 11.573700 5.309100 # O
98 33 2 0.556400 2.360650 10.852800 4.677420 # H
99 33 2 0.556400 1.246180 11.339800 5.622280 # H
100 34 1 -1.112800 9.475430 0.348874 4.098120 # O
101 34 2 0.556400 8.884690 -0.244864 3.347450 # H
102 34 2 0.556400 10.054100 0.774503 3.600670 # H
103 35 1 -1.112800 0.010520 6.679330 6.084480 # O
104 35 2 0.556400 0.046652 7.214860 6.876490 # H
105 35 2 0.556400 0.310100 7.241510 5.330880 # H
106 36 1 -1.112800 6.153230 4.948680 5.715680 # O
107 36 2 0.556400 6.347170 5.425750 6.507980 # H
108 36 2 0.556400 6.681400 4.134080 5.619610 # H
109 37 1 -1.112800 3.898970 10.122100 1.533400 # O
110 37 2 0.556400 4.479990 10.910500 1.499800 # H
111 37 2 0.556400 3.858400 10.101700 0.579605 # H
112 38 1 -1.112800 11.506200 3.204840 10.861000 # O
113 38 2 0.556400 10.597600 3.222960 11.028100 # H
114 38 2 0.556400 11.546500 2.434670 10.319100 # H
115 39 1 -1.112800 10.677900 4.338840 6.172880 # O
116 39 2 0.556400 11.342100 4.987790 6.277110 # H
117 39 2 0.556400 11.105000 3.454520 6.329560 # H
118 40 1 -1.112800 11.269000 10.402200 8.967430 # O
119 40 2 0.556400 11.945700 9.669490 8.817430 # H
120 40 2 0.556400 11.392200 10.972400 9.673550 # H
121 41 1 -1.112800 9.015520 6.819390 9.590060 # O
122 41 2 0.556400 8.480310 7.447960 9.075890 # H
123 41 2 0.556400 8.772660 5.864390 9.537090 # H
124 42 1 -1.112800 9.156080 7.043630 6.079910 # O
125 42 2 0.556400 9.786990 6.368220 6.462160 # H
126 42 2 0.556400 8.637950 7.287850 6.807400 # H
127 43 1 -1.112800 8.023320 10.118300 2.593470 # O
128 43 2 0.556400 8.835280 9.772450 3.075270 # H
129 43 2 0.556400 8.319480 10.174900 1.654080 # H
130 44 1 -1.112800 11.458700 11.363500 6.215150 # O
131 44 2 0.556400 10.817600 10.742100 5.830830 # H
132 44 2 0.556400 11.362800 11.032500 7.071230 # H
133 45 1 -1.112800 7.501170 8.687200 7.619310 # O
134 45 2 0.556400 6.987900 9.210670 6.875940 # H
135 45 2 0.556400 7.775980 9.294880 8.278630 # H
136 46 1 -1.112800 12.163200 7.636940 3.306910 # O
137 46 2 0.556400 11.905500 7.001590 2.634400 # H
138 46 2 0.556400 13.143695 7.878660 3.172600 # H
139 47 1 -1.112800 3.855820 9.856260 8.038060 # O
140 47 2 0.556400 4.106300 10.648500 7.785770 # H
141 47 2 0.556400 4.004960 10.015200 9.060490 # H
142 48 1 -1.112800 11.959100 11.106700 12.207400 # O
143 48 2 0.556400 11.627900 11.064000 13.164333 # H
144 48 2 0.556400 12.908351 10.710100 12.287100 # H
145 49 1 -1.112800 5.215880 4.825910 11.379400 # O
146 49 2 0.556400 5.091530 3.935540 11.648000 # H
147 49 2 0.556400 4.395040 5.172330 11.674300 # H
148 50 1 -1.112800 3.447470 6.263900 5.322950 # O
149 50 2 0.556400 2.953140 6.002480 4.629230 # H
150 50 2 0.556400 4.256030 5.710520 5.184060 # H
151 51 1 -1.112800 9.252860 6.955710 2.103340 # O
152 51 2 0.556400 9.635100 6.201610 2.627900 # H
153 51 2 0.556400 8.511360 7.033430 2.773840 # H
154 52 1 -1.112800 7.010900 2.690190 8.051850 # O
155 52 2 0.556400 7.205340 2.906420 7.186290 # H
156 52 2 0.556400 5.978790 2.609760 8.151220 # H
157 53 1 -1.112800 7.593650 5.241530 12.303700 # O
158 53 2 0.556400 7.778320 6.013730 11.866800 # H
159 53 2 0.556400 6.619420 5.032550 12.146000 # H
160 54 1 -1.112800 8.311930 4.384830 9.775160 # O
161 54 2 0.556400 8.029970 3.742280 9.209050 # H
162 54 2 0.556400 7.710280 4.412850 10.689200 # H
163 55 1 -1.112800 0.216025 8.259980 11.000200 # O
164 55 2 0.556400 -0.771200 8.207870 11.179900 # H
165 55 2 0.556400 0.405663 7.364710 10.808500 # H
166 56 1 -1.112800 5.092650 3.345230 2.380140 # O
167 56 2 0.556400 4.289880 3.402320 2.037290 # H
168 56 2 0.556400 5.195870 4.270950 2.448160 # H
169 57 1 -1.112800 8.415280 0.433228 9.468590 # O
170 57 2 0.556400 8.232370 -0.590000 9.181410 # H
171 57 2 0.556400 7.890330 0.865852 8.788890 # H
172 58 1 -1.112800 1.521980 12.261800 10.252200 # O
173 58 2 0.556400 2.313870 12.717497 9.819640 # H
174 58 2 0.556400 0.740191 12.869956 10.193400 # H
175 59 1 -1.112800 5.046090 0.042758 7.210720 # O
176 59 2 0.556400 4.465450 0.143690 6.438300 # H
177 59 2 0.556400 6.007220 0.148100 6.995730 # H
178 60 1 -1.112800 8.116110 11.951600 6.522740 # O
179 60 2 0.556400 8.877920 11.978800 5.875040 # H
180 60 2 0.556400 7.461260 11.374300 6.175280 # H
181 61 1 -1.112800 7.559250 2.393910 5.322680 # O
182 61 2 0.556400 8.225370 1.772280 4.928820 # H
183 61 2 0.556400 6.701890 2.109310 4.957270 # H
184 62 1 -1.112800 2.306480 9.941070 11.436600 # O
185 62 2 0.556400 1.774970 9.157100 11.271100 # H
186 62 2 0.556400 1.870360 10.613100 10.942200 # H
187 63 1 -1.112800 3.674940 1.236140 9.165420 # O
188 63 2 0.556400 4.256920 0.800629 8.426150 # H
189 63 2 0.556400 3.551770 2.121820 8.663390 # H
190 64 1 -1.112800 6.313260 8.030800 0.560737 # O
191 64 2 0.556400 7.065380 7.786980 0.801491 # H
192 64 2 0.556400 6.039630 8.846740 1.106740 # H

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
57 1 85 86
58 1 85 87
59 1 88 89
60 1 88 90
61 1 91 92
62 1 91 93
63 1 94 95
64 1 94 96
65 1 97 98
66 1 97 99
67 1 100 101
68 1 100 102
69 1 103 104
70 1 103 105
71 1 106 107
72 1 106 108
73 1 109 110
74 1 109 111
75 1 112 113
76 1 112 114
77 1 115 116
78 1 115 117
79 1 118 119
80 1 118 120
81 1 121 122
82 1 121 123
83 1 124 125
84 1 124 126
85 1 127 128
86 1 127 129
87 1 130 131
88 1 130 132
89 1 133 134
90 1 133 135
91 1 136 137
92 1 136 138
93 1 139 140
94 1 139 141
95 1 142 143
96 1 142 144
97 1 145 146
98 1 145 147
99 1 148 149
100 1 148 150
101 1 151 152
102 1 151 153
103 1 154 155
104 1 154 156
105 1 157 158
106 1 157 159
107 1 160 161
108 1 160 162
109 1 163 164
110 1 163 165
111 1 166 167
112 1 166 168
113 1 169 170
114 1 169 171
115 1 172 173
116 1 172 174
117 1 175 176
118 1 175 177
119 1 178 179
120 1 178 180
121 1 181 182
122 1 181 183
123 1 184 185
124 1 184 186
125 1 187 188
126 1 187 189
127 1 190 191
128 1 190 192

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
27 1 80 79 81
28 1 83 82 84
29 1 86 85 87
30 1 89 88 90
31 1 92 91 93
32 1 95 94 96
33 1 98 97 99
34 1 101 100 102
35 1 104 103 105
36 1 107 106 108
37 1 110 109 111
38 1 113 112 114
39 1 116 115 117
40 1 119 118 120
41 1 122 121 123
42 1 125 124 126
43 1 128 127 129
44 1 131 130 132
45 1 134 133 135
46 1 137 136 138
47 1 140 139 141
48 1 143 142 144
49 1 146 145 147
50 1 149 148 150
51 1 152 151 153
52 1 155 154 156
53 1 158 157 159
54 1 161 160 162
55 1 164 163 165
56 1 167 166 168
57 1 170 169 171
58 1 173 172 174
59 1 176 175 177
60 1 179 178 180
61 1 182 181 183
62 1 185 184 186
63 1 188 187 189
64 1 191 190 192

data文件导入到VMD显示问题
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