[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).
>
>
> Over what range is your interaction defined? If the potential isn't zero by
> the time you get to the relevant cutoff, then you will produce artefacts.
>
>
> I use same 6,12 table  in Gromacs top folder, which goes to 1+rc.



> > 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?
> >
>
> If the interaction isn't in the list, it doesn't get computed.
>

>
I hope you got my point. I assume when I define rcut-off in .mdp file, the
resulted potential should be zero after this value, so the larger rlist >
rcut-off wont make difference. 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.

So the solution for me now is to put the potential in the table file to
zero manually for x>cut-off. But it is better to solve the problem in
Gromacs.

> 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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