[gmx-users] Intra molecular force correction for SPME

[Mark Abraham]

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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