[gmx-users] Intra molecular force correction for SPME
mark.j.abraham at gmail.com
Thu Jun 5 22:04:33 CEST 2014
ewald_LRcorrection in gmxlib/ewald_util.c (for the group scheme). Aliens
probably handle it for the Verlet scheme, for all I know ;-)
On Thu, Jun 5, 2014 at 9:15 PM, Sumith YD <ydsumith at gmail.com> wrote:
> 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
> CAMNuMARoDamXRqBd5cNOif8uskapcv56+fEOP5W7qNng0Qp7jQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 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
> > 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.
> > 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
> > > 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
> > > the source code. I tried the mail archive and Google search but
> > > exactly locate/find anything helpful. Pardon me if this question was
> > > 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
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