[gmx-users] R: Re: User tabulated potentials with cutoff-scheme = verlet, GROMACS 5.0.1 and 5.0.2

[Mark Abraham]

On Thu, Oct 2, 2014 at 1:13 PM, Francesco Mambretti <
francesco.mambretti at studenti.unimi.it> wrote:

> So then, you have to update the pages on your website (
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential)
> about tabulated potentials,


Indeed, I have fixed that. Unfortunately, much of the Gromacs documentation
precedes the existence of the Verlet scheme, and we have not made a
systematic attempt to update all of it.


> and also in the user manual (5.0.1 version).
>

Noted


> Otherwise, people risks misleading about this topic!
> In fact, I spent my last month in learning GROMACS, encouraged by the
> documentation about tabulated potentials (it seems so easy to do that!),
> and nothing is said about the cutoff scheme you have to use! And also the
> attached pdf should be updated.
>

That would be up to the user who contributed it, unfortunately.

This is a very strong limit, LJ and Buckingham potentials are often not so
> accurate potentials, if you really want to simulate physical systems.
>
> So the alternatives I have are:
> 1) use group charge (e.g.: I have 108 atoms of mixed Ar and Kr, and each
> of them is a group charge) and group cutoff - but the run will require more
> time
>

I'd expect that a tiny VDW-only system like that will show little to no
performance difference between the cutoff schemes (assuming the group
scheme setup is buffered), because both make about the same use of SIMD
intrinsics and the effect spent in optimizing for your kind of systems is
about the same in both. Once tables work in Verlet, I'd expect even less
difference between the two (but GPU support will be great for larger
systems).

2) downgrade my GROMACS version, so that I am not forced to use verlet
> cutoff if I want a configuration that

scales fast
>

You're not forced to use Verlet now ;-) The default scheme changed in 5,
but the group scheme is still there (and works better than ever). There's
zero value in using an earlier version.

Mark

3) use LJ potential
>
> Am I right?
>
> Francesco
>
> Il 02/10/14, Mark Abraham  <mark.j.abraham at gmail.com> ha scritto:
> > On Thu, Oct 2, 2014 at 11:58 AM, Francesco Mambretti <
> > francesco.mambretti at studenti.unimi.it> wrote:
> >
> > > Dear all, I am a student in Physics at Milan University. For my
> thesis, I
> > > should run a simulation of a binary liquid mixture of Argon and
> Krypton.
> > >
> > > Until now, I have been learning how to use GROMACS (version 5.0.1 and,
> > > since
> > > yesterady, 5.0.2) essentials, and my simulations were all based on LJ
> > > potential, and all was fine.
> > >
> > > Now I want to use a tabulated potential, that is a more detailed
> potential,
> > > different in form from LJ, taken from literature.
> > > I followed the steps of the instructions on GROMACS website
> > > (
> > >
> http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials?highlight=tabulated+potential
> > > )
> > > and the attached pdf, but it doesn't work.
> > > I ought to use cutoff-scheme = verlet (because the "group" scheme does
> not
> > > make sense, because my system has no charge),
> >
> >
> > VDW-only systems work fine in the group scheme, e.g. with a single atom
> per
> > charge group - but you will need to organize your own details for
> adequate
> > buffering.
> >
> >
> > > but I receive these errors
> > > from grompp:
> > >
> > > ERROR 1 [file Aziz.mdp]:
> > > With Verlet lists only cut-off and PME LJ interactions are supported
> > >
> > >
> > > ERROR 2 [file Aziz.mdp]:
> > > With Verlet lists only cut-off, reaction-field, PME and Ewald
> > > electrostatics are supported
> > >
> > > Aziz.mdp is my mdp file, that contains the instructions coulombtype =
> User
> > > and vdwtype = User.
> > >
> > > What am I missing?
> > > Or it is true that GROMACS is not able to use user-defined potentials
> with
> > > verlet's cutoff? This would be a serious handicap for this code!
> > > Am I forced to use charge groups?
> > >
> >
> > For now, yes. There is work in progress to implement user tables for the
> > Verlet scheme (& GPUs). Some help with alpha-stage testing would be very
> > welcome! But for that, you might like to have a working group-scheme
> setup
> > against which to validate.
> >
> > Mark
> >
> >
> > > Thanks in advance,
> > >
> > > Francesco Mambretti - University of Milan - LCP (Parallel Computing
> Lab)
> > >
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