[gmx-users] rlist- group scheme

Mark Abraham mark.j.abraham at gmail.com
Fri Jan 19 20:09:50 CET 2018


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.


On Fri, Jan 19, 2018, 14:25 Faezeh Pousaneh <fpoosaneh at 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list