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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
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
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