[gmx-users] rlist- group scheme

[Faezeh Pousaneh]

For any range of cut off it gives wrong results for rlist>rcut-off.

Now I understand where the problem comes.  I tried to see the collisions of
two molecules with a table (user potential). From the resulted LJ potential
between two particles I see that it takes the potential to zero at rlist,
not at rcut-off.
how to deal with it now?


Best regards


On Sun, Jan 21, 2018 at 12:57 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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