Mark Abraham mark.j.abraham at gmail.com
Thu Jan 30 21:47:58 CET 2014

On Jan 30, 2014 8:09 PM, "MUSYOKA THOMMAS" <mutemibiochemistry at gmail.com>
> Dear Users,
> I have been doing 10 ns MD simulations of protein-ligand complexes on a
> local cluster of 64 cores using GROMACS 4.5.7. However, there seems to be
> no much difference in the time it takes to complete one cycle of an mdrun
> (3-days - same as when I used a machine with 4 cores).
> Will be appreciative to know if its possible shorten the time period.

Probably, but not without inspecting the diagnostics in the log file and
knowing a lot more about your hardware and simulation. Some clues can be
found in stage 5 of
GROMACS 4.5.7 doors not support OpenMP and there will be many minor

Or switch to 4.6.5 and get a free ~30% faster just for showing up...


> See the following command that I have incorporated in a python script so
> to automate the  md process right from the beginning.
>                         md="md.mdp"
> os.system(mdscriptcopy)
> finalmdruncommand="grompp -f %s -c %s -t %s -p %s -n %s -o %s"%
> (md,nptgro,nvtcpt,topoltop,indexfile,mdtpr)
> os.system(finalmdruncommand)
> *finalrun="mdrun -v -deffnm md"*
> os.system(finalrun)
> *"Do all the good you can, By all the means you can, In all the ways you
> can, In all the places you can,At all the times you can,To all the people
> you can,As long as ever you can." - John Wesley. *
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