[gmx-users] Anybody using Silica InterfaceFF on Gromacs?

Mark Abraham mark.j.abraham at gmail.com
Mon Jul 3 02:04:05 CEST 2017


On Fri, Jun 30, 2017 at 2:46 AM Alex <nedomacho at gmail.com> wrote:

> >
> >
> >>
> >> He he, childish :)
> >
> > David, no offense intended. I just think that when applied to solids, the
> entire concept of what works so well for biomolecular systems becomes a bit
> of a joke. And vice versa, to be fair. Spoken from experience, really -- we
> here used Gromacs to simulate things that I keep telling people not to
> simulate with Gromacs, and it got published!. :)

Sure - one should use a tool capable of doing the job, and use its optional
capabilities accordingly. Choosing non-bonded exclusions based on bonds, in
a way that does not implement the intended model physics, is indeed wrong,
but that doesn't make the use of modified 1-4 pair interactions "childish"
in general ;-)

> In any case, I second what was said above re: # of exclusions. Solid-state
> potentials use smooth drop-offs to exclude long-range interactions between
> close neighbor sharing elements, so looking into David's suggestion may in
> fact fix the issues immediately.

So, for the record, the actual issue is that GROMACS does not implement
some kind of tapering of non-bonded interactions that would apply between
particle pairs at short range?


> Alex
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