[gmx-users] rlist- group scheme

[Mark Abraham]

Hi,

There could be. But over what range does your table work correctly? What do
you get when you have a two particle system at various displacements?

Mark

On Fri, Jan 19, 2018, 23:59 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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.abraham at 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 <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
> > > --
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