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
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 ...
"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.
Mark
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