[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
-------------- next part --------------
[ 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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