[gmx-users] MD SIMULATIONS ON A CLUSTER

[Mark Abraham]

On Jan 30, 2014 8:09 PM, "MUSYOKA THOMMAS" <mutemibiochemistry at gmail.com>
wrote:
>
> 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
http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2c_%22What's_in_a_log_file%22%2c_basic_performance_improvements%3a_Mark_Abraham%2c_Session_1Abut
GROMACS 4.5.7 doors not support OpenMP and there will be many minor
differences.

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

Mark

> See the following command that I have incorporated in a python script so
as
> 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
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