[gmx-users] rlist- group scheme

[Faezeh Pousaneh]

Hi Mark,

For rlist=rcut-off (max one) it works correctly, but as soon as rlist>
rcut-off it fails and gives different energies. Which I do not understand
why. In principle, there is nothing going on after cut-off in potentials.




Best regards


On Sat, Jan 20, 2018 at 1:13 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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