[gmx-users] About extracting the non-bonded forces

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 24 23:05:24 CET 2018


On Wed, Jan 24, 2018 at 10:05 PM Lovuit CHEN <lovuitchen at outlook.com> wrote:

> Hello everyone,
> I was trying to export non-bonded forces (e.g. LJ, Coulomb) from GROMACS
> during MD simulations, for post-processing of personal projects. But I am
> not sure where to look at. I heard the non-bonded forces are calculated
> with assembly loops, do I have access to them? Which places in the
> installation directory should I look at?

First advice: don't, because force fields have not been parametrized such
that they mean anything. But creative use of multiple mdrun -rerun and
choices of energy groups can produce some decompositions of the total force.

> Also, in the case of small non-bonded interactions (like 2 orders of
> magnitude smaller to bonded forces), how much difference it make for my
> simulation if I just remove the [pairs] directive in the topology input
> file?

Who can say?

(I am using GROMACS 4.5, BTW, I couldn't upgrade to the latest because the
> research group did heavy customization on this version)

Don't, unless you're using those modifications (and then maybe still
don't... there's 7 years of bug fixes you're missing out on...)


> Thank you very much!
> Lovuit
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