[gmx-users] rlist- group scheme
fpoosaneh at gmail.com
Fri Jan 19 23:58:06 CET 2018
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.
On Fri, Jan 19, 2018 at 8:09 PM, Mark Abraham <mark.j.abraham at gmail.com>
> 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.
> > 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
> > 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
> > --
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