[gmx-users] Problem to simulate silica melts and amorphous silica with BKS potentials

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 10 12:33:49 CET 2009

David Waroquiers wrote:
> 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
> 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 ...

"Generation" refers to the process described in (probably) chapter 4 of 
the manual where all possible pairwise interactions between a set of 
atom types are calculated from generic parameters characteristic of the 
two atom types involved (see your [atomtypes] entries). An alternative 
is to describe the pairwise interactions specifically, as you have done. 
Thus GROMACS didn't need to generate any, and reports this fact.


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