[gmx-users] problem by start with grompp
Alexej Mazheika
alex.mazheika at gmail.com
Thu Jan 3 13:34:28 CET 2013
Dear all!
I'm new with Gromacs.
I prepared some job for it but I cann't start with grompp. It writes me
"Fatal error:
Something is wrong in the coordinate formatting of file conf.gro. Note that
gro is fixed format (see the manual)".
What is wrong? I want to calculate a silver cluster contining 125 atoms.
And the conf.gro file was prepared according to on-line manual of Gromacs.
Input-files (conf.gro, topol.top and silver.itp) are shown below.
Thank you in advance,
Alex
*conf.gro:*
Bulk silver, t = 0.0
125
Cluster Ag 1 0.000 0.000 0.000 0.3549 0.4758
-0.0904
Cluster Ag 2 0.204 0.204 0.000 0.5023 0.6171
-0.1193
Cluster Ag 3 0.409 0.409 0.000 0.1706 1.9242
-0.1299
Cluster Ag 4 -0.409 -0.409 0.000 0.1853 -0.0977
0.2463
Cluster Ag 5 -0.204 -0.204 0.000 -0.1168
-0.0371 0.9161
Cluster Ag 6 0.204 0.000 0.204 -0.0551 1.4850
-0.1296
Cluster Ag 7 0.409 0.204 0.204 0.3101 -0.3484
-0.0008
Cluster Ag 8 0.613 0.409 0.204 0.5298 0.4809
0.2331
Cluster Ag 9 -0.204 -0.409 0.204 -0.4401
-0.3946 1.5223
Cluster Ag 10 0.000 -0.204 0.204 -0.0845
-0.0352 -0.6628
Cluster Ag 11 0.409 0.000 0.409 -0.5423 0.5471
-0.3902
Cluster Ag 12 0.613 0.204 0.409 -3.1280 0.3170
-1.0229
Cluster Ag 13 0.817 0.409 0.409 0.6789 0.0640
-0.0344
Cluster Ag 14 0.000 -0.409 0.409 -0.1302 0.1578
-0.0127
Cluster Ag 15 0.204 -0.204 0.409 0.6698 1.0679
-1.3227
Cluster Ag 16 -0.409 0.000 -0.409 -0.2256
-0.3632 0.0514
Cluster Ag 17 -0.204 0.204 -0.409 0.2069
-0.2388 0.6106
Cluster Ag 18 0.000 0.409 -0.409 0.7349 1.3763
-0.9274
Cluster Ag 19 -0.817 -0.409 -0.409 -0.9525
-0.2627 0.4172
Cluster Ag 20 -0.613 -0.204 -0.409 0.5542
-0.4907 -0.0019
Cluster Ag 21 -0.204 0.000 -0.204 1.2732 1.4340
-0.3768
Cluster Ag 22 0.000 0.204 -0.204 0.0591 -0.1353
-0.5894
Cluster Ag 23 0.204 0.409 -0.204 -0.5937
-0.1721 0.0862
Cluster Ag 24 -0.613 -0.409 -0.204 0.4257
2.1061 0.2350
Cluster Ag 25 -0.409 -0.204 -0.204 0.2298
-0.0775 0.3642
Cluster Ag 26 0.000 0.204 0.204 -0.0384 0.0506
-0.0643
Cluster Ag 27 0.204 0.409 0.204 -1.2260 2.3805
-0.4377
Cluster Ag 28 0.409 0.613 0.204 0.3871 -0.0963
-0.0275
Cluster Ag 29 -0.409 -0.204 0.204 0.3262
-0.1153 -0.1338
Cluster Ag 30 -0.204 0.000 0.204 0.9592 -0.5738
-0.0823
Cluster Ag 31 0.204 0.204 0.409 0.5413 0.4476
-0.0550
Cluster Ag 32 0.409 0.409 0.409 -0.3161 -0.2168
-0.1527
Cluster Ag 33 0.613 0.613 0.409 -0.6814 0.5993
-0.2307
Cluster Ag 34 -0.204 -0.204 0.409 0.2552 0.4818
-0.0729
Cluster Ag 35 0.000 0.000 0.409 0.0408 0.0414
-0.0155
Cluster Ag 36 0.409 0.204 0.613 -0.8836 -0.7443
0.2603
Cluster Ag 37 0.613 0.409 0.613 -0.2645 -0.3151
-0.2842
Cluster Ag 38 0.817 0.613 0.613 -0.2692 -0.2904
-0.2710
Cluster Ag 39 0.000 -0.204 0.613 0.7939 -0.8404
0.2681
Cluster Ag 40 0.204 0.000 0.613 -0.9573 -0.0950
-0.1476
Cluster Ag 41 -0.409 0.204 -0.204 -0.0251
0.1413 0.8754
Cluster Ag 42 -0.204 0.409 -0.204 0.2609 2.5060
-0.0260
Cluster Ag 43 0.000 0.613 -0.204 0.0891 -0.0179
-0.5820
Cluster Ag 44 -0.817 -0.204 -0.204 0.0411
-0.1423 -0.0371
Cluster Ag 45 -0.613 0.000 -0.204 2.3046
-0.1273 -0.3149
Cluster Ag 46 -0.204 0.204 0.000 0.1441 0.1891
0.4334
Cluster Ag 47 0.000 0.409 0.000 0.1110 -0.0916
-0.3021
Cluster Ag 48 0.204 0.613 0.000 1.7741 0.8838
-0.5496
Cluster Ag 49 -0.613 -0.204 0.000 -0.5728
0.6002 0.5888
Cluster Ag 50 -0.409 0.000 0.000 -0.3661 0.1889
-0.3877
Cluster Ag 51 0.000 0.409 0.409 -0.9799 -0.9920
-0.7041
Cluster Ag 52 0.204 0.613 0.409 0.5592 0.5398
0.2283
Cluster Ag 53 0.409 0.817 0.409 0.2324 0.0219
0.8539
Cluster Ag 54 -0.409 0.000 0.409 -1.4993 2.1205
-0.7097
Cluster Ag 55 -0.204 0.204 0.409 -0.3122 0.1147
0.0698
Cluster Ag 56 0.204 0.409 0.613 -0.0068 0.7304
-0.0835
Cluster Ag 57 0.409 0.613 0.613 1.3374 -0.3369
-0.8824
Cluster Ag 58 0.613 0.817 0.613 0.1708 0.0097
0.3006
Cluster Ag 59 -0.204 0.000 0.613 0.2412 -0.0100
0.3912
Cluster Ag 60 0.000 0.204 0.613 -0.2191 -0.1492
0.6027
Cluster Ag 61 0.409 0.409 0.817 0.1502 -0.1929
0.0553
Cluster Ag 62 0.613 0.613 0.817 0.0980 -0.2419
0.0734
Cluster Ag 63 0.817 0.817 0.817 0.5492 -0.3666
-1.9324
Cluster Ag 64 0.000 0.000 0.817 -0.1240 -0.0202
-0.4686
Cluster Ag 65 0.204 0.204 0.817 -0.7004 -0.5690
0.2006
Cluster Ag 66 -0.409 0.409 0.000 -1.5054
-0.7691 -2.3209
Cluster Ag 67 -0.204 0.613 0.000 -0.2158 0.3046
0.1285
Cluster Ag 68 0.000 0.817 0.000 -0.2796 -0.1991
-0.1788
Cluster Ag 69 -0.817 0.000 0.000 -0.9589
-0.5213 1.1579
Cluster Ag 70 -0.613 0.204 0.000 0.2821 -0.1943
-0.2747
Cluster Ag 71 -0.204 0.409 0.204 0.2847 -0.0926
-0.0396
Cluster Ag 72 0.000 0.613 0.204 0.9786 -0.8756
0.0956
Cluster Ag 73 0.204 0.817 0.204 -0.4605 -0.0901
-0.1077
Cluster Ag 74 -0.613 0.000 0.204 -0.1979
-0.4105 -0.0193
Cluster Ag 75 -0.409 0.204 0.204 -0.7589
-1.6968 1.2298
Cluster Ag 76 0.000 -0.409 -0.409 0.2119 0.8203
-0.0629
Cluster Ag 77 0.204 -0.204 -0.409 -0.3306
-1.1357 -0.0166
Cluster Ag 78 0.409 0.000 -0.409 0.3747 0.7404
-1.7866
Cluster Ag 79 -0.409 -0.817 -0.409 0.6604
-0.3262 -0.4982
Cluster Ag 80 -0.204 -0.613 -0.409 0.0260
0.2726 0.5296
Cluster Ag 81 0.204 -0.409 -0.204 -1.1697
0.0510 -1.4964
Cluster Ag 82 0.409 -0.204 -0.204 -0.2341
-0.0474 0.0546
Cluster Ag 83 0.613 0.000 -0.204 -0.4170
-0.1297 -0.0042
Cluster Ag 84 -0.204 -0.817 -0.204 -0.4506
0.5506 0.4995
Cluster Ag 85 0.000 -0.613 -0.204 -0.0199
0.2624 -0.4591
Cluster Ag 86 0.409 -0.409 0.000 -0.5095
-0.1720 -0.2808
Cluster Ag 87 0.613 -0.204 0.000 -1.4552
-0.2619 -0.0281
Cluster Ag 88 0.817 0.000 0.000 0.1955 -0.6831
0.5407
Cluster Ag 89 0.000 -0.817 0.000 0.3588 0.3660
-0.0230
Cluster Ag 90 0.204 -0.613 0.000 -0.1350 0.4515
-1.3540
Cluster Ag 91 -0.409 -0.409 -0.817 -0.1335
-0.5718 0.5483
Cluster Ag 92 -0.204 -0.204 -0.817 -0.3027
0.1857 0.5561
Cluster Ag 93 0.000 0.000 -0.817 -1.4709
-0.4135 0.4452
Cluster Ag 94 -0.817 -0.817 -0.817 -0.0143
0.0735 -0.2719
Cluster Ag 95 -0.613 -0.613 -0.817 -0.0585
-0.3216 -0.5952
Cluster Ag 96 -0.204 -0.409 -0.613 -1.2468
-3.2206 0.5695
Cluster Ag 97 0.000 -0.204 -0.613 0.4107 0.1953
0.4603
Cluster Ag 98 0.204 0.000 -0.613 0.3280 -0.1838
0.1072
Cluster Ag 99 -0.613 -0.817 -0.613 -0.3420
-1.2584 1.4216
Cluster Ag 100 -0.409 -0.613 -0.613 -0.5109
-0.3568 -0.3184
Cluster Ag 101 0.000 -0.204 -0.204 0.4185
1.0431 0.1785
Cluster Ag 102 0.204 0.000 -0.204 -0.3009
2.1678 3.1545
Cluster Ag 103 0.409 0.204 -0.204 0.3822
-0.5026 0.1695
Cluster Ag 104 -0.409 -0.613 -0.204 0.1886
0.0421 0.0337
Cluster Ag 105 -0.204 -0.409 -0.204 0.6404
0.5121 2.6134
Cluster Ag 106 0.204 -0.204 0.000 -0.5949
-0.5280 -0.5255
Cluster Ag 107 0.409 0.000 0.000 -0.3757
-0.0529 -0.0024
Cluster Ag 108 0.613 0.204 0.000 -1.0720
-0.0008 -0.1236
Cluster Ag 109 -0.204 -0.613 0.000 -0.5689
-0.0252 -0.0757
Cluster Ag 110 0.000 -0.409 0.000 -0.3944
0.6959 -0.0330
Cluster Ag 111 0.409 -0.204 0.204 -1.5810
1.9547 1.0041
Cluster Ag 112 0.613 0.000 0.204 0.1659 0.5399
0.6711
Cluster Ag 113 0.817 0.204 0.204 -0.4301 0.6907
-0.0736
Cluster Ag 114 0.000 -0.613 0.204 -0.0391
-2.3133 0.1403
Cluster Ag 115 0.204 -0.409 0.204 -0.2787
-0.2522 -0.1074
Cluster Ag 116 -0.409 -0.204 -0.613 -0.2086
-0.4636 0.2368
Cluster Ag 117 -0.204 0.000 -0.613 -0.3764
-0.8997 0.4974
Cluster Ag 118 0.000 0.204 -0.613 0.1786 0.2621
-0.3673
Cluster Ag 119 -0.817 -0.613 -0.613 0.5404
0.3315 -0.3523
Cluster Ag 120 -0.613 -0.409 -0.613 0.9744
0.4829 0.2210
Cluster Ag 121 -0.204 -0.204 -0.409 -0.3398
0.0290 0.1140
Cluster Ag 122 0.000 0.000 -0.409 -0.1941
0.2379 -1.1315
Cluster Ag 123 0.204 0.204 -0.409 -1.0682
-0.6024 -1.3417
Cluster Ag 124 -0.613 -0.613 -0.409 -0.3698
0.0429 0.2879
Cluster Ag 125 -0.409 -0.409 -0.409 -0.3682
0.2570 0.5603
2.00000 2.00000 2.00000
*topol.top:*
#include "amber03.ff/forcefield.itp"
#include "silver.itp"
[ moleculetype ]
Cluster 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 Ag 1 Cluster Ag 1 0.000
2 Ag 1 Cluster Ag 2 0.000
3 Ag 1 Cluster Ag 3 0.000
4 Ag 1 Cluster Ag 4 0.000
5 Ag 1 Cluster Ag 5 0.000
6 Ag 1 Cluster Ag 6 0.000
7 Ag 1 Cluster Ag 7 0.000
8 Ag 1 Cluster Ag 8 0.000
9 Ag 1 Cluster Ag 9 0.000
10 Ag 1 Cluster Ag 10 0.000
11 Ag 1 Cluster Ag 11 0.000
12 Ag 1 Cluster Ag 12 0.000
13 Ag 1 Cluster Ag 13 0.000
14 Ag 1 Cluster Ag 14 0.000
15 Ag 1 Cluster Ag 15 0.000
16 Ag 1 Cluster Ag 16 0.000
17 Ag 1 Cluster Ag 17 0.000
18 Ag 1 Cluster Ag 18 0.000
19 Ag 1 Cluster Ag 19 0.000
20 Ag 1 Cluster Ag 20 0.000
21 Ag 1 Cluster Ag 21 0.000
22 Ag 1 Cluster Ag 22 0.000
23 Ag 1 Cluster Ag 23 0.000
24 Ag 1 Cluster Ag 24 0.000
25 Ag 1 Cluster Ag 25 0.000
26 Ag 1 Cluster Ag 26 0.000
27 Ag 1 Cluster Ag 27 0.000
28 Ag 1 Cluster Ag 28 0.000
29 Ag 1 Cluster Ag 29 0.000
30 Ag 1 Cluster Ag 30 0.000
31 Ag 1 Cluster Ag 31 0.000
32 Ag 1 Cluster Ag 32 0.000
33 Ag 1 Cluster Ag 33 0.000
34 Ag 1 Cluster Ag 34 0.000
35 Ag 1 Cluster Ag 35 0.000
36 Ag 1 Cluster Ag 36 0.000
37 Ag 1 Cluster Ag 37 0.000
38 Ag 1 Cluster Ag 38 0.000
39 Ag 1 Cluster Ag 39 0.000
40 Ag 1 Cluster Ag 40 0.000
41 Ag 1 Cluster Ag 41 0.000
42 Ag 1 Cluster Ag 42 0.000
43 Ag 1 Cluster Ag 43 0.000
44 Ag 1 Cluster Ag 44 0.000
45 Ag 1 Cluster Ag 45 0.000
46 Ag 1 Cluster Ag 46 0.000
47 Ag 1 Cluster Ag 47 0.000
48 Ag 1 Cluster Ag 48 0.000
49 Ag 1 Cluster Ag 49 0.000
50 Ag 1 Cluster Ag 50 0.000
51 Ag 1 Cluster Ag 51 0.000
52 Ag 1 Cluster Ag 52 0.000
53 Ag 1 Cluster Ag 53 0.000
54 Ag 1 Cluster Ag 54 0.000
55 Ag 1 Cluster Ag 55 0.000
56 Ag 1 Cluster Ag 56 0.000
57 Ag 1 Cluster Ag 57 0.000
58 Ag 1 Cluster Ag 58 0.000
59 Ag 1 Cluster Ag 59 0.000
60 Ag 1 Cluster Ag 60 0.000
61 Ag 1 Cluster Ag 61 0.000
62 Ag 1 Cluster Ag 62 0.000
63 Ag 1 Cluster Ag 63 0.000
64 Ag 1 Cluster Ag 64 0.000
65 Ag 1 Cluster Ag 65 0.000
66 Ag 1 Cluster Ag 66 0.000
67 Ag 1 Cluster Ag 67 0.000
68 Ag 1 Cluster Ag 68 0.000
69 Ag 1 Cluster Ag 69 0.000
70 Ag 1 Cluster Ag 70 0.000
71 Ag 1 Cluster Ag 71 0.000
72 Ag 1 Cluster Ag 72 0.000
73 Ag 1 Cluster Ag 73 0.000
74 Ag 1 Cluster Ag 74 0.000
75 Ag 1 Cluster Ag 75 0.000
76 Ag 1 Cluster Ag 76 0.000
77 Ag 1 Cluster Ag 77 0.000
78 Ag 1 Cluster Ag 78 0.000
79 Ag 1 Cluster Ag 79 0.000
80 Ag 1 Cluster Ag 80 0.000
81 Ag 1 Cluster Ag 81 0.000
82 Ag 1 Cluster Ag 82 0.000
83 Ag 1 Cluster Ag 83 0.000
84 Ag 1 Cluster Ag 84 0.000
85 Ag 1 Cluster Ag 85 0.000
86 Ag 1 Cluster Ag 86 0.000
87 Ag 1 Cluster Ag 87 0.000
88 Ag 1 Cluster Ag 88 0.000
89 Ag 1 Cluster Ag 89 0.000
90 Ag 1 Cluster Ag 90 0.000
91 Ag 1 Cluster Ag 91 0.000
92 Ag 1 Cluster Ag 92 0.000
93 Ag 1 Cluster Ag 93 0.000
94 Ag 1 Cluster Ag 94 0.000
95 Ag 1 Cluster Ag 95 0.000
96 Ag 1 Cluster Ag 96 0.000
97 Ag 1 Cluster Ag 97 0.000
98 Ag 1 Cluster Ag 98 0.000
99 Ag 1 Cluster Ag 99 0.000
100 Ag 1 Cluster Ag 100 0.000
101 Ag 1 Cluster Ag 101 0.000
102 Ag 1 Cluster Ag 102 0.000
103 Ag 1 Cluster Ag 103 0.000
104 Ag 1 Cluster Ag 104 0.000
105 Ag 1 Cluster Ag 105 0.000
106 Ag 1 Cluster Ag 106 0.000
107 Ag 1 Cluster Ag 107 0.000
108 Ag 1 Cluster Ag 108 0.000
109 Ag 1 Cluster Ag 109 0.000
110 Ag 1 Cluster Ag 110 0.000
111 Ag 1 Cluster Ag 111 0.000
112 Ag 1 Cluster Ag 112 0.000
113 Ag 1 Cluster Ag 113 0.000
114 Ag 1 Cluster Ag 114 0.000
115 Ag 1 Cluster Ag 115 0.000
116 Ag 1 Cluster Ag 116 0.000
117 Ag 1 Cluster Ag 117 0.000
118 Ag 1 Cluster Ag 118 0.000
119 Ag 1 Cluster Ag 119 0.000
120 Ag 1 Cluster Ag 120 0.000
121 Ag 1 Cluster Ag 121 0.000
122 Ag 1 Cluster Ag 122 0.000
123 Ag 1 Cluster Ag 123 0.000
124 Ag 1 Cluster Ag 124 0.000
125 Ag 1 Cluster Ag 125 0.000
[ bonds ]
1 2 5
[ system ]
Bulk silver
[ molecules ]
Cluster 1
*silver.itp:*
[ atomtypes ]
; type mass charge ptype c6 c12
Ag 107.8682 0.0 A 2.6169e-3 2.5231e-6
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