[gmx-users] MD SIMULATIONS ON A CLUSTER
mutemibiochemistry at gmail.com
Thu Jan 30 19:50:35 CET 2014
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.
finalmdruncommand="grompp -f %s -c %s -t %s -p %s -n %s -o %s"%
*finalrun="mdrun -v -deffnm md"*
*"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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