Hi, On Fri, Jun 30, 2017 at 2:46 AM Alex <nedoma...@gmail.com> wrote:
> > > > > >> > >> He he, childish :) > > > > David, no offense intended. I just think that when applied to solids, the > entire concept of what works so well for biomolecular systems becomes a bit > of a joke. And vice versa, to be fair. Spoken from experience, really -- we > here used Gromacs to simulate things that I keep telling people not to > simulate with Gromacs, and it got published!. :) > Sure - one should use a tool capable of doing the job, and use its optional capabilities accordingly. Choosing non-bonded exclusions based on bonds, in a way that does not implement the intended model physics, is indeed wrong, but that doesn't make the use of modified 1-4 pair interactions "childish" in general ;-) > In any case, I second what was said above re: # of exclusions. Solid-state > potentials use smooth drop-offs to exclude long-range interactions between > close neighbor sharing elements, so looking into David's suggestion may in > fact fix the issues immediately. > So, for the record, the actual issue is that GROMACS does not implement some kind of tapering of non-bonded interactions that would apply between particle pairs at short range? Mark > Alex > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
