[gmx-users] soft-core potential in combination with PME

Jeroen van Bemmelen J.J.M.vanBemmelen at tnw.tudelft.nl
Thu Apr 12 22:42:45 CEST 2007

Thanks a lot, Berk. This is exactly the answer I was hoping for, 
meaning it's clear for me now.


> Date: Thu, 12 Apr 2007 13:42:42 +0200
> From: "Berk Hess" <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] soft-core potential in combination with PME
> 	(sorry,	again)
> To: gmx-users at gromacs.org
> Message-ID: <BAY110-F244D3EF7714D1CB3CA3BBB8E5E0 at phx.gbl>
> Content-Type: text/plain; format=flowed
> I don't know about Anwars paper.
> But I can say that their is no fundamental difference between PME
> and RF with soft-core. With the GROMACS setup they converge
> to exactly the same energies at any lambda value when you increase the RF 
> cut-off.
> I don't understand what David Mobley meant exactly.
> There is no Coulomb singularity with soft-core.
> Maybe one could have an unfortunate situation where the LJ
> is already very soft, but the Coulomb not very soft,
> which could lead to instabilities.
> But I have never encountered this.
> Berk.
> >From: "Jeroen van Bemmelen" <J.J.M.vanBemmelen at tnw.tudelft.nl>
> >Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >To: gmx-users at gromacs.org
> >Subject: RE: [gmx-users] soft-core potential in combination with PME 
> >(sorry,again)
> >Date: Thu, 12 Apr 2007 12:38:56 +0200
> >
> >Hi Berk (and others),
> >
> >Thanks a lot for your quick answer. And sorry to bother you again
> >with this long email, but I still feel I'm missing something really
> >essential here.
> >
> >I agree that in essence the convergence and the singularity are two
> >different problems. And if I understand you correctly, my first
> >conclusion (that it's completely fine to use soft-core together with
> >PME, that it takes care of the singularity problem, both for the VDW
> >and the electrostatic part at the same time, and that it does not
> >lead to additional problems) was right. So numerical instabilities
> >(simulation crash) during free energy calculations resulting from
> >singularities (overlapping atoms) should not be an issue with ANY
> >type of electrostatics method in GROMACS (even PME), just as long as
> >you use the soft-core potential.
> >
> >But in that case I really don't understand why Anwar claims in his
> >aforementioned paper that the electrostatics singularity problem is
> >only solved by the standard soft-core potential for the simple
> >truncation and reaction field schemes, and not for PME. And why David
> >Mobley mentions numerical instabilities caused by "charge-charge
> >overlap" (e.g. in http://www.gromacs.org/pipermail/gmx-users/2006-
> >March/020785.html and other mails) while using soft-core. Are the
> >mentioned numerical instabilities (simulation blowing up) resulting
> >from charge overlap not a direct consequence of the singularity at
> >r=0? And is the soft-core potential not supposed to take care of
> >exactly THIS problem, by effectively limiting the forces as r-->0? At
> >least that's how I understand it from the Beutler paper and from the
> >manual.
> >
> >So I guess somebody is wrong here, most likely I myself, and I hope
> >you or someone else can clarify this a bit further.
> >
> >Thanks,
> >Jeroen

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