[gmx-users] decreased performance with free energy

[Szilárd Páll]

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.

--
Szilárd


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
> --
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