[gmx-users] GMX-PLUMED speed

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Sun Feb 5 23:08:46 CET 2017

Interesting finding. Have you tried leaving out the two options
independently? Also would be good to try that with gromacs-2016.

What is your system size and cluster usage? This sounds a phenomenal speed
as well as speed up.

You should probably share this on the plumed google group too.

Best wishes

> Dears,
> I am using gromacs v5.1.4 with PLUMED v2.3.0.
> Through my experience as a novice in using PLUMED, I have noticed that not
> writing the restraint/forces info in a file and not using a STRIDE
> accelerate the code significantly.
> Using a line such as follows in the plumed parameters set:
> PRINT ARG=restraint.bias
> instead of the most correct:
> PRINT STRIDE=10000 ARG=restraint.bias FILE=bias
> would make gmx run at 950 ns/day instead of 550 ns/day.
> The inconvenient is that the log file becomes large (all the restraint are
> written in it) and messy (the values are mixing with the rest of the info
> on exchanges), but the speed up is considerable.
> Note that I still print the values of the restraint in a file, which I
> haven’t tried to remove but it could also speed up the run.
> Someone should may be look at this as he speed up applies on XX replicas
> so lots of CPU time (cooling system, energy, climat change, …) is
> wasted.
> I hope this helps.
> X-
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