[gmx-users] Gromacs Version 5.0.2 - Bug #1603

[Mark Abraham]

On Wed, Oct 8, 2014 at 8:24 PM, Siva Dasetty <sdasett at g.clemson.edu> wrote:

> Thank You Mark for the reply.
>
> Now that clears my confusion about the values in the PP-PME load part of
> the log file. However, I am still a little bit confused about how to
> distinguish between a normal-but-not-guranteed change and the normal
> change,


They're the same thing. It is normal that rcoulomb changes as a result of
tuning. But it is not guaranteed to be changed - depends on your simulation
setup, CPU, network, phase of the moon...


> though I understood that for a normal change we can compare the
> densities obtained from GPU runs and the CPU only runs to verify the
> results.
>
> Also, I have a general question about using vdwtype as PME.
>
> Is it advisable to use vdwtype as PME when I am using GPU runs?
>

That's two questions in one. LJ-PME with the Verlet scheme runs on GPUs.
Whether your simulation should use LJ-PME depends on whether you judge that
the effects of inaccurate treatment of long-range inhomogeneity would be
noticeable in your system. You should check out the papers cited in the
GROMACS manual (and one more is submitted). I personally think the decision
is a no-brainer for a membrane+protein system, for example. But for
calculating the free-energy of solvation of methanol in water... probably
immaterial.

Mark


> Thanks.
>
> On Wed, Oct 8, 2014 at 12:42 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On Wed, Oct 8, 2014 at 4:29 PM, Siva Dasetty <sdasett at g.clemson.edu>
> > wrote:
> >
> > > Dear All,
> > >
> > > I am using gpu enabled gromacs version 5.0.2 and I am checking if my
> > > simulation is still affected by bug #1603
> > > http://redmine.gromacs.org/issues/1603.
> > >
> > > Below is the PP-PME load balancing part of my log file
> > >
> > >  PP/PME load balancing changed the cut-off and PME settings:
> > >            particle-particle                    PME
> > >             rcoulomb  rlist            grid      spacing   1/beta
> > >    initial  1.000 nm  1.092 nm     108 108 120   0.119 nm  0.320 nm
> > >    final    1.482 nm  1.574 nm      72  72  80   0.178 nm  0.475 nm
> > >  cost-ratio           3.00             0.30
> > >  (note that these numbers concern only part of the total PP and PME
> load)
> > >
> > > The release notes says,
> > >
> > > If, for your simulation, the final rcoulomb value (1.368 here) is
> > different
> > > from the initial one (1.000 here), then so was the LJ cutoff for
> > > short-ranged interactions, and the model physics was not what you asked
> > > for.
> > >
> > > Does that mean the initial and final values are supposed to be the
> same?
> > >
> >
> > No. The point of the tuning is to change the rcoulomb value to maximize
> > performance while maintaining the quality of the electrostatic
> > approximation you chose in the .mdp file. If you were using one of the
> > affected versions (5.0 or 5.0.1), then the normal-but-not-guaranteed
> change
> > of rcoulomb led to an inappropriate change of rvdw, which is why it is a
> > relevant diagnostic for whether an actual simulation from the versions
> with
> > wrong code was affected in practice.
> >
> > But the normal change of rcoulomb neither confirms nor denies that the
> bug
> > is fixed in 5.0.2. You could observe that the NPT density in 5.0.2 agrees
> > with a CPU-only (or 4.6.x GPU) calculation, for example.
> >
> > Mark
> > --
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>
>
> --
> Siva
> --
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