Dear Mark, Thank you, however, the problem occurs when 'table' is used. For vdWtype=not-user the energies are OK and the same for both cases, as I mentioned. So I guess there should be something wrong in the way Gromacs interpolates the table with cutoffs and rlist.
Best regards Best regards On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > With the group scheme, when you choose nstlist > 1 then you get a list of > all the groups that satisfy rlist, whatever it is, and continue to use that > list for the whole lifetime. If you chose rlist==rcoulomb, then rcoulomb is > never considered again, because you chose to use an unbuffered list. But > with rlist > rcoulomb, you chose the list to have interactions that are not > within rcoulomb, so every interaction is checked at every step for whether > it is within rcoulomb, before including it. That's slower to run, but a > better approach. And of course you can't expect them to compute the same > numbers, particularly if things move fast relative to the buffer size and > list lifetime. > > The Verlet scheme defaults do a good job of automating all this, but as you > know, there's not yet support for tabulated interactions. > > Mark > > On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > > > Hi, > > > > I run a simple example using Table,6,12 (for LJ) with vdW type= user. > Then > > group scheme should be chosen. > > > > In results, I got different LJ energies when I set rlist=rcoulomb and > > rlist>rcoulomb (which is allowed in this scheme). I see in the manual > that > > with group scheme that can be happen. But I do not find how to get rid of > > the differences in energies? or which rlist is the case. > > > > However, when I run with vdW type= cutoff for both rlist rlist=rcoulomb > > and rlist>rcoulomb with group scheme I get similar results. > > > > Best regards > > -- > > 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. > -- 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.
