[gmx-users] rlist- group scheme

Faezeh Pousaneh fpoosaneh at gmail.com
Tue Jan 23 18:26:56 CET 2018 

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.


>
> 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
> > > > > > > > > > --
> > > > > > > > > > Gromacs Users mailing list
> > > > > > > > > >
> > > > > > > > > > * Please search the archive at
> > > > > > > > > >
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > > > before
> > > > > > > > > > posting!
> > > > > > > > > >
> > > > > > > > > > * Can't post? Read
> > > > http://www.gromacs.org/Support/Mailing_Lists
> > > > > > > > > >
> > > > > > > > > > * For (un)subscribe requests visit
> > > > > > > > > > https://maillist.sys.kth.se/
> mailman/listinfo/gromacs.org_
> > > > > gmx-users
> > > > > > > or
> > > > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Gromacs Users mailing list
> > > > > > > > >
> > > > > > > > > * Please search the archive at
> > http://www.gromacs.org/Support
> > > > > > > > > /Mailing_Lists/GMX-Users_List before posting!
> > > > > > > > >
> > > > > > > > > * Can't post? Read http://www.gromacs.org/Support
> > > /Mailing_Lists
> > > > > > > > >
> > > > > > > > > * For (un)subscribe requests visit
> > > > > > > > >
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > > > or
> > > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > > >
> > > > > > > > --
> > > > > > > > Gromacs Users mailing list
> > > > > > > >
> > > > > > > > * Please search the archive at
> > > > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> > > before
> > > > > > > > posting!
> > > > > > > >
> > > > > > > > * Can't post? Read
> > http://www.gromacs.org/Support/Mailing_Lists
> > > > > > > >
> > > > > > > > * For (un)subscribe requests visit
> > > > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx
> > > -users
> > > > > or
> > > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > > >
> > > > > > > --
> > > > > > > Gromacs Users mailing list
> > > > > > >
> > > > > > > * Please search the archive at http://www.gromacs.org/
> > > > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > > > >
> > > > > > > * Can't post? Read http://www.gromacs.org/
> Support/Mailing_Lists
> > > > > > >
> > > > > > > * For (un)subscribe requests visit
> > > > > > >
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > > > or
> > > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > > >
> > > > > > --
> > > > > > Gromacs Users mailing list
> > > > > >
> > > > > > * Please search the archive at
> > > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
> before
> > > > > > posting!
> > > > > >
> > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > > >
> > > > > > * For (un)subscribe requests visit
> > > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_
> gmx-users
> > > or
> > > > > > send a mail to gmx-users-request at gromacs.org.
> > > > > >
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at http://www.gromacs.org/
> > > > > Support/Mailing_Lists/GMX-Users_List before posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> > or
> > > > > send a mail to gmx-users-request at gromacs.org.
> > > > >
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>

More information about the gromacs.org_gmx-users mailing list