[gmx-users] rlist- group scheme

Wed Jan 24 13:57:39 CET 2018

>
> Hi again,
>

> 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, I thinks there has been misunderstanding. I never saw zero
interactions.

What I mean is: with a LJ table 6,12 given in Gromacs page (even my own
other user tables), when I take rlist=0.6 and rvdw=0.5 in .mdp file, the
resulted potential from simulation shows that instead of potential becomes
zero at rvdW=0.5, it gets zero at rlist=0.6. So many unwanted interactions
are counted.   Which is an important point to know about Gromacs fails
here.

It is OK as long as rvdw-off=rcoulmb=rlist. But if we have a case with
rvdW<rcoulomb, it fails. That is why, in order to avoid that I should
change the table manually to insert rvdW smoothly to zero.

> 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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