[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials
David Waroquiers
david.waroquiers at uclouvain.be
Tue Mar 10 12:08:27 CET 2009
Hello
I'm trying to simulate amorphous SiO2 with the use of the BKS potentials
(van Beest, B. W. H.; Kramer, G. J. & van Santen, R. A. - Phys. Rev.
Lett., American Physical Society, 1990, 64, 1955-1958).
According to these potentials, I should use the Buckingham potentials
with user-defined parameters plus a coulomb part with user-defined
charges for each atom type. I don't need any other forcefield from
GROMACS.
When I try to preprocess my topology file and get the .tpr binary file
in order to start the simulation, I get the following message in the
terminal :
processing topology...
Generated 0 of the 3 non-bonded parameter combinations
Excluding 0 bonded neighbours molecule type 'O'
Excluding 0 bonded neighbours molecule type 'Si'
I don't understand why my non-bonded parameters aren't generated ...
My topol.top (this is one inspired from one I found in this forum) and
conf.gro files are attached.
Maybe I should disable the Gromacs forcefields in the grompp.mdp file ?
I'm new to GROMACS so any advice is welcome :-)
David Waroquiers - PhD Student
Université Catholique de Louvain
Laboratoire de Physico-Chimie et de Physique des Matériaux
European Theoretical Spectroscopy Facility
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Silica
72
1O O 1 0.404 0.377 0.833 0.0422 -0.0023 0.1380
2O O 2 0.433 0.243 0.390 0.0473 0.0243 0.1557
3O O 3 0.628 0.840 0.683 0.2954 0.0850 -0.0137
4O O 4 0.179 0.139 0.034 -0.0552 0.0421 0.0942
5O O 5 0.501 0.300 0.131 -0.0016 -0.0704 -0.0518
6O O 6 0.667 0.348 0.975 0.1603 -0.0185 -0.1492
7O O 7 0.934 0.313 0.669 -0.0170 -0.0390 -0.0321
8O O 8 0.481 0.203 0.675 -0.0109 -0.0106 0.1098
9O O 9 0.042 0.514 0.282 -0.0023 0.0278 -0.0179
10O O 10 0.581 0.655 0.500 0.0271 -0.0086 -0.0018
11O O 11 0.506 0.159 0.937 0.1370 0.0336 0.1897
12O O 12 0.085 0.450 0.520 0.0488 0.0707 -0.0262
13O O 13 0.753 0.040 0.623 -0.1945 -0.0319 -0.1393
14O O 14 0.315 0.937 0.343 0.0028 0.1022 -0.0027
15O O 15 0.881 0.729 0.118 -0.1587 0.0237 0.0398
16O O 16 0.683 0.621 0.251 0.0616 -0.0072 0.0438
17O O 17 0.129 0.100 0.298 0.0446 -0.2673 0.2269
18O O 18 0.041 0.014 0.881 0.2950 0.0320 -0.0435
19O O 19 0.628 0.489 0.775 0.0110 0.0104 -0.1048
20O O 20 0.877 0.436 0.878 -0.2041 0.0886 0.0809
21O O 21 1.017 0.690 0.465 -0.0082 0.2018 0.0220
22O O 22 0.288 0.082 0.492 0.1297 -0.1041 0.2055
23O O 23 0.450 0.728 0.302 0.1020 -0.0243 0.0193
24O O 24 0.262 0.305 0.220 0.0471 0.1527 -0.0085
25O O 25 0.919 0.984 0.051 -0.0197 0.0333 -0.1554
26O O 26 0.683 0.129 0.098 -0.2149 0.2352 -0.1939
27O O 27 0.862 0.858 0.579 -0.1010 0.0507 -0.0364
28O O 28 0.275 0.135 0.822 -0.0158 -0.0694 -0.0080
29O O 29 0.053 0.182 0.520 0.0737 -0.0125 0.0033
30O O 30 0.064 0.267 0.869 -0.0409 -0.0712 -0.0181
31O O 31 0.936 0.882 0.313 0.0636 -0.0017 -0.0690
32O O 32 0.477 0.476 0.315 0.0289 -0.0565 0.1165
33O O 33 0.220 0.671 0.402 -0.0402 0.0067 0.0031
34O O 34 0.544 0.026 0.479 -0.0121 0.0998 -0.0247
35O O 35 0.851 0.467 0.157 -0.1350 0.0551 -0.0146
36O O 36 0.442 0.425 0.590 0.0576 0.0327 -0.0059
37O O 37 0.741 0.077 0.350 -0.0974 -0.0599 0.1233
38O O 38 0.827 0.940 0.835 0.0780 -0.2107 0.0562
39O O 39 0.443 0.642 0.729 0.0361 -0.1063 0.0729
40O O 40 0.396 0.809 0.539 -0.1232 0.1032 -0.3219
41O O 41 0.709 0.596 1.011 -0.0269 -0.0230 -0.0058
42O O 42 0.875 0.161 0.892 -0.0367 -0.1671 0.0745
43O O 43 0.929 0.347 0.393 -0.0348 -0.0506 0.1373
44O O 44 0.007 0.281 0.165 0.0888 -0.2050 -0.0918
45O O 45 0.717 0.916 0.186 -0.0321 -0.0365 0.0833
46O O 46 0.648 0.262 0.507 -0.1611 0.1586 0.0029
47O O 47 0.499 0.042 0.248 0.0569 -0.0612 -0.0768
48O O 48 0.067 0.948 0.494 -0.1914 -0.2485 -0.0491
49Si Si 49 0.766 0.921 0.688 -0.0653 0.0939 -0.0358
50Si Si 50 0.687 0.106 0.499 0.1484 -0.1689 0.0386
51Si Si 51 0.594 0.231 0.020 -0.0485 -0.1935 0.0937
52Si Si 52 0.330 0.788 0.391 0.0515 -0.0400 0.0536
53Si Si 53 0.977 0.845 0.467 0.0060 -0.1095 0.0162
54Si Si 54 0.093 0.579 0.421 -0.0064 0.1717 0.0311
55Si Si 55 0.415 0.210 0.817 0.0014 0.0523 -0.0235
56Si Si 56 0.965 0.399 0.242 0.0835 0.0979 -0.0785
57Si Si 57 1.011 0.324 0.531 -0.0432 -0.0969 0.0546
58Si Si 58 0.408 0.039 0.387 -0.0242 -0.0076 0.0033
59Si Si 59 0.556 0.615 0.344 -0.1230 -0.0379 -0.0927
60Si Si 60 0.915 0.007 0.928 -0.0324 0.1534 -0.0120
61Si Si 61 0.779 0.606 0.125 0.0343 0.0485 -0.0521
62Si Si 62 0.469 0.487 0.738 -0.0127 0.0201 -0.0797
63Si Si 63 0.658 0.029 0.219 0.0682 0.0213 0.0840
64Si Si 64 0.872 0.880 0.166 0.0022 -0.0813 -0.0170
65Si Si 65 0.144 0.133 0.907 0.0121 0.0903 0.0103
66Si Si 66 0.414 0.339 0.258 0.0552 0.0420 -0.0598
67Si Si 67 0.941 0.299 0.830 0.0869 -0.0327 -0.0119
68Si Si 68 0.492 0.285 0.536 -0.0486 0.0283 -0.0074
69Si Si 69 0.723 0.478 0.903 0.0255 -0.0254 0.0208
70Si Si 70 0.515 0.744 0.622 -0.0329 -0.0651 0.0720
71Si Si 71 0.134 0.058 0.455 -0.0658 0.1744 -0.0952
72Si Si 72 0.146 0.201 0.175 -0.0724 0.0322 -0.1041
1.03008 1.03008 1.03008
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[ defaults ]
2 1 ; Buckingam potential
[ atomtypes ]
; name mass charge ptype c6 c12
O 15.99940 -1.200 A 0.22617E-02 0.74158E-06 0.0000;
Si 28.08000 2.400 A 0.14738E-01 0.22191E-04 0.0000;
[ nonbond_params ]
O O 2 1.339973E+5 27.6 1.688507E-2
O Si 2 1.737112E+6 48.7318 1.288457E-2
Si Si 2 0 0 0
[ moleculetype ]
O 0
[ atoms ]
1 O 1 O O 1 -1.2 15.99940
[ moleculetype ]
Si 0;
[ atoms ]
1 Si 1 Si Si 2 2.4 28.08000
[ system ]
Silica
[ molecules ]
O 48
Si 24
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