ha salem wrote:
dear user
my molecule is HSA it has about 120000 atoms its not small I run the
calculation
with
mpirun -np 4 /usr/local/share/gromacs_331/bin/mdrun -f topol.tpr o
md.trr -c md_out.gro -e md.edr -g md.log &
then I run top and I see 4 cores are working but the time of calculation
is the same without
-np 4 option
You need to pay much closer attention to the options to mdrun. "-f" does
nothing, you've not used "-s", you've omitted the hyphen from your "-o
md.trr", and you've not told mdrun to run in parallel using -np. See
http://wiki.gromacs.org/index.php/grompp#Parallel_calculations
Mark
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