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 [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
