[gmx-users] Extension on different machines (CPU/GPU

Mark Abraham mark.j.abraham at gmail.com
Tue Jun 5 10:43:13 CEST 2018


You'll basically never get a reproducible trajectory
http://www.gromacs.org/Documentation/Terminology/Reproducibility. If your
conclusions would depend on the configurations in any single trajectory,
you'll have a hard time demonstrating that those conclusions are valid
reflection of reality.


On Tue, Jun 5, 2018 at 10:37 AM Nicolas Cheron <
nicolas.cheron.boulot at gmail.com> wrote:

> Dear all,
> I ran a 250ns simulation with Gromacs 5.1.2 on a machine with only CPUs. I
> then wanted to extend the simulation to 300ns, and copied the .tpr and the
> .cpt to another machine with GPUs (also running Gromacs 5.1.2). I observed
> strange results, so I decided to also extend the simulation (from 250ns) on
> the first machine to compare.
> Different results are obtained for the 2 extensions (that were started from
> the same .tpr and .cpt) on the 2 different machines/architectures. Is it a
> known behaviour, and one should never proceed like this? Is it due to
> CPU/GPU, or only the fact that machines are different and the same would
> have happened on another CPU machine?
> Thank you
> Nicolas
> PS: I am looking at a solute in a water:glycerol mixture. By "different
> results" I mean that the number of water (or glycerol) around the solute
> are different at all time steps
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