[gmx-users] GMX-PLUMED speed

XAvier Periole x.periole at rug.nl
Sun Feb 5 09:50:03 CET 2017


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.

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