[gmx-users] decreased performance with free energy

[David de Sancho]

Thanks Szilárd
I have posted both in the Gist below for the free energy simulation
https://gist.github.com/daviddesancho/4abdc0d40e2355671ead7f8e40283b57
May it have to do with the number of particles in the box that are affected
by the typeA -> typeB change?

David


Date: Wed, 17 Jul 2019 17:09:21 +0200
> From: Szil?rd P?ll <pall.szilard at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] decreased performance with free energy
> Message-ID:
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> CANnYEw4usZxnnwZ56tZbqSJwkT3Cu7Pf+8hhFXa6nFUg0o7U_g at mail.gmail.com>
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>
> Hi,
>
> Lower performe especially with GPUs is not unexpected, but what you report
> is unusually large. I suggest you post your mdp and log file, perhaps there
> are some things to improve.
>
> --
> Szil?rd
>
>
> On Wed, Jul 17, 2019 at 3:47 PM David de Sancho <david.desancho at ehu.eus>
> wrote:
>
> > Hi all
> > I have been doing some testing for Hamiltonian replica exchange using
> > Gromacs 2018.3 on a relatively simple system with 3000 atoms in a cubic
> > box.
> > For the modified hamiltonian I have simply modified the water
> interactions
> > by generating a typeB atom in the force field ffnonbonded.itp with
> > different parameters file and then creating a number of tpr files for
> > different lambda values as defined in the mdp files. The only difference
> > between mdp files for a simple NVT run and for the HREX runs are the
> > following lines:
> >
> > > ; H-REPLEX
> > > free-energy = yes
> > > init-lambda-state = 0
> > > nstdhdl                 = 0
> > > vdw_lambdas = 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
> >
> > I have tested for performance in the same machine and compared the
> standard
> > NVT run performance (~175 ns/day in 8 cores) with that for the free
> energy
> > tpr file (6.2 ns/day).
> > Is this performance loss what you would expect or are there any immediate
> > changes you can suggest to improve things? I have found a relatively old
> > post on this on Gromacs developers (
> https://redmine.gromacs.org/issues/742
> > ),
> > but I am not sure whether it is the exact same problem.
> > Thanks,
> >
> > David
> > --
> > Gromacs Users mailing list
>