[gmx-users] GMX-PLUMED speed

Justin Lemkul jalemkul at vt.edu
Sun Feb 5 17:19:54 CET 2017

On 2/5/17 3:49 AM, XAvier Periole wrote:
> 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.

Have you reported this to the PLUMED forum?  They'll certainly want to know (and 
it's probably more applicable there, anyway).



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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