[gmx-users] rlist- group scheme

Wed Jan 24 13:35:29 CET 2018

Hi,

On Tue, Jan 23, 2018 at 6:27 PM Faezeh Pousaneh <fpoosaneh at gmail.com> wrote:

> Hi Mark,
> thanks for remarks, just one point:
>
>
> > > But what I see from resulted potential vs
> > > displacement of two molecules, is that Gromacs has taken the potential
> to
> > > zero at rlist not *''rcut-off''*. That is why for rcut-off > rlist the
> > > result is not correct.
> > >
> >
> > You're seeing the consequence of the particles at displacement > rlist
> not
> > being put into the list, so not making a contribution.
> >
>
> no, I see the particles between rcut-off and rlist  which should have no
> contribution to the potential (since potential should be zero after cut-off
> and rlist is bigger than rcutoff) *have* contributions, and that is what
> makes the wrong results.
>

Yes. But I thought your comment was referring to "taking the potential to
zero." Neither the cutoff implementation nor your table was doing that at
rcutoff, so any particle in the list got computed regardless of rcutoff.
When you saw a zero-strength interaction, that was because the particles
weren't being put in the list, and not because it was in the list and
evaluated as zero strength.

Mark

> So the solution for me now is to put the potential in the table file to
> > > zero manually for x>cut-off.
> >
> >
> > Glancing at the kernels that implement user tables, that's what you
> should
> > do. That means the forces are strange and you would wish to consider a
> form
> > where the potential smoothly reaches zero at the cutoff.
> >
> > But it is better to solve the problem in
> > > Gromacs.
> > >
> >
> > It looks like the group scheme with user tables doesn't have support for
> > buffered lists with a correct cutoff. That correct cutoff is only
> available
> > in the group scheme for potentials that do go to zero. Likely we
> concluded
> > that because you have the ability to express your wishes entirely in your
> > table, you should do so. Or use rlist == rvdw == rcoulomb.
> >
> > Mark
> >
> > > Mark
> > > >
> > > >
> > > > >
> > > > >
> > > > > 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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