[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

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 

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?


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