[gmx-users] soft-core potential in combination with PME (sorry, again)
Jeroen van Bemmelen
J.J.M.vanBemmelen at tnw.tudelft.nl
Thu Apr 12 01:44:41 CEST 2007
After reading several posts on this subject on the mailing list, I'm
still a bit confused.
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
However, from several discussions on this mailing list (e.g.
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?
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