Thanks a lot, Berk. This is exactly the answer I was hoping for, meaning it's clear for me now.
Jeroen > Date: Thu, 12 Apr 2007 13:42:42 +0200 > From: "Berk Hess" <[EMAIL PROTECTED]> > Subject: RE: [gmx-users] soft-core potential in combination with PME > (sorry, again) > To: [EMAIL PROTECTED] > Message-ID: <[EMAIL PROTECTED]> > 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" <[EMAIL PROTECTED]> > >Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]> > >To: [EMAIL PROTECTED] > >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 _______________________________________________ gmx-users mailing list [EMAIL PROTECTED] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
