[gmx-users] Intra molecular force correction for SPME

[Sumith YD]

Dear Mark,
For the paper please refer "
http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf".
While calculating the forces in SPC/E water, H-O, H-H forces in the same
molecule will be calculated in reciprocal space due to the property of
Particle Mesh technique. Do you mean to say that this will be compensated
by SHAKE/SETTLE? Won't it affect the net force acting on the molecule if we
don't remove it?

Sumith YD


Date: Wed, 4 Jun 2014 21:26:31 +0200
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: Discussion list for GROMACS users
        <gromacs.org_gmx-users at maillist.sys.kth.se>
Subject: Re: [gmx-users] Intra molecular force correction for SPME
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        <CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s=Tr5eX0jdN3enA at mail.gmail.com>
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On Wed, Jun 4, 2014 at 6:52 PM, Sumith YD <ydsumith at gmail.com> wrote:

> Dear gromacs community,
>
> How does the gromacs calculate Intra molecular force correction (To
correct
> the unwanted intra molecular force in Fourier space especially for rigid
> molecules)? I couldn't find that information listed anywhere in the
manual.
> I could find some details from "Publications by Thierry Matthey- PhD
> thesis".


Where is that?

But I couldn't find gromacs citing it and hence just curious to
> know is there any other reference which gromacs uses?
> I am also having a hard time to locate intramolecular force correction in
> the source code. I tried the mail archive and Google search but couldn't
> exactly locate/find anything helpful. Pardon me if this question was asked
> earlier and answered.
>

GROMACS doesn't implement rigid molecules except inasmuch as they can be
expressed through holonomic constraints on bonds and angles (or frozen
atoms). As such, the forces are projected out (respectively, zeroed), so
the question does not arise.

Mark


> Sumith
> Mechanical Engineer, Syracuse University.
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