[gmx-users] Getting non-bonded forces from GROMACS

[James]

Hi Mark,

Thanks a lot for the input. I understand what you mean about additive force
fields, or at least I think I do, so let me summarize what I think is the
point:

In an additive force field, you have a lot of parameters that can be tuned,
and the objective is to tune them in such a way that they reproduce
experimental (or higher level of theory) results. Since adjusting one
parameter can affect the tuning of others, you can't discretely map the
force field parameters to real-world physical phenomena. So, attempting to
decompose an additive force field to get, for example, VDW forces, is, at
least mathematically speaking, incorrect. If that is the idea, let me make
a couple observations, and then ask a question.

1) The force field does have parameters whose mathematical forms are chosen
to be representative of real-world phenomenon, such as LJ potentials.

2) In some sense, some force field parameters may actually be used
"separately" in certain simulation settings -- which, practically speaking,
seems like an example of decomposition. For example, beyond the cutoff
distance, VDW plays no role. But, if you bring two structures close to each
other they experience VDW forces and react appropriately (or so we hope).
The bonded forces didn't change (did they?), so it seems like if you can
model something without VDW, and something with VDW, then it is legitimate
to consider VDW a separate force that can be added or removed as
appropriate.

So, my question is this: While I understand that it may not be
mathematically rigorous, does decomposing the force field really give
meaningless answers (i.e., does not "correlate with something physical")? I
could see it not being as accurate as desired, but for it to be useless
seems strange to me.

Sincerely,
James


> Message: 4
> Date: Tue, 24 Sep 2019 18:57:42 +0200
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: GROMACS Listserv <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] Getting non-bonded forces from GROMACS
> Message-ID:
>         <CAMNuMATjcy=
> noOji5ZC71iMknV53O+r3KzVbV_NLP8Y4ziYLTQ at mail.gmail.com>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi,
>
> You can make a version of your topology without the bonded interactions,
> regenerate the tpr and use gmx mdrun -rerun. But there is no force field
> for which this is known to be useful for any purpose (ie correlate with
> something physical). Additive force fields are not built to be decomposable
> in this way.
>
> Mark
>
> On Tue, 24 Sep 2019 at 04:38, James <james at ryley.com> wrote:
>
> > Hi,
> >
> > I am interested in getting only non-bonded force vectors on each atom in
> an
> > MD run. I know "gmx traj -of" (or "gmx traj -af" -- what's the
> difference?)
> > will output total forces on atoms, as will "gmx trajectory -of". But, is
> > there a way to only get non-bonded forces?
> >
> > Sincerely,
> > James Ryley
> > --
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