[gmx-users] Intra molecular force correction for SPME

[Sumith YD]

Dear Mark,

Thank you so much for the clarification. I will try to locate that equation
in the source code too.

Sumith YD.


Date: Thu, 5 Jun 2014 20:43:03 +0200
From: Mark Abraham <mark.j.abraham at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Intra molecular force correction for SPME
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        <CAMNuMARoDamXRqBd5cNOif8uskapcv56+fEOP5W7qNng0Qp7jQ at mail.gmail.com>
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On Jun 4, 2014 10:04 PM, "Sumith YD" <ydsumith at gmail.com> wrote:
>
> Dear Mark,
> For the paper please refer "
> http://www.ii.uib.no/~matthey/text/mattheyPhD.pdf".

That's just restating standard stuff, e.g. Essman 1995.

> 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?

I thought you were referring to larger rigid bodies. Bonded exclusions are
dealt with by all these codes the same way. Note carefully the use of erf
vs erfc in the corrective terms.

Mark

> 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
> Message-ID:
>         <CAMNuMATfDXtbztpO8isPubzU709mDkjLLv3s=
Tr5eX0jdN3enA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> 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.
> > --

-- 
thanks & regards,
Sumith YD