[gmx-users] rlist- group scheme

[Mark Abraham]

Hi,

Yes, you said that before. But I asked what range it worked over, ie what
range of cutoff.

Mark

On Sat, Jan 20, 2018, 17:15 Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> 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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