[gmx-users] MD SIMULATIONS ON A CLUSTER

[MUSYOKA THOMMAS]

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.

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)








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