[gmx-users] soft-core potential in combination with PME (sorry, again)

[Berk Hess]

Soft-core interactions are fully supported with PME.
Both mails you quote do not state otherwise.

The second mail refers to convergence issues when
switching off LJ as well as electrostatics interactions.
This problem will (probably) always be present, and has
nothing to do with the singularities in the potentials,
but with the fact that one often has awkward free energy
landscapes at intermediate states.

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: [gmx-users] soft-core potential in combination with PME 
>(sorry,again)
>Date: Thu, 12 Apr 2007 01:44:41 +0200
>
>Hi all,
>
>After reading several posts on this subject on the mailing list, I'm
>still a bit confused.
>
>In http://www.gromacs.org/pipermail/gmx-users/2005-
>October/017691.html it is more or less suggested that the
>implementation of the soft-core potential for free energy
>calculations in combination with PME is relatively straightforward,
>and is comparable to its implementation when using other treatments
>of long range electrostatics. In addition, the GROMACS manual does
>not mention any differences or problems when using this combination.
>So from this I cautiously conclude that it's fine to use soft-core
>together with PME, that it takes care of the singularity problem (as
>soft-core should), and that it does not lead to additional problems
>(at least not compared to its use with other electrostatic
>treatments).
>
>However, from several discussions on this mailing list (e.g.
>http://www.gromacs.org/pipermail/gmx-users/2006-June/022388.html) I
>understand there are indeed problems when using this combination of
>parameters. Not only could it lead to convergence problems (which
>could be prevented by using a 3-stage strategy), but it could also
>lead to stability problems because of the singularity at r=0 (for
>which the soft-core potential was invented in the first place).
>Moreover, reference was made to an article by Anwar (J. Chem. Phys.,
>122, 224117 (2005)), according to which soft-core in combination with
>PME is still a no-go (unless you use Anwars method, which is
>significantly different from the standard GROMACS soft-core
>implementation). So from this I conclude that the soft-core potential
>for PME has NOT been implemented into GROMACS yet, or at least not in
>a way that solves the singularity problem sufficiently, which is
>contradicting my earlier conclusion.
>
>Obviously, I'm missing or misinterpreting something here. But could
>someone please clear up this subject for me?
>
>Thanks,
>Jeroen
>_______________________________________________
>gmx-users mailing list    gmx-users at gromacs.org
>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 gmx-users-request at gromacs.org.
>Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Play online games with your friends with Messenger 
http://www.join.msn.com/messenger/overview