[gmx-users] run parallel

[Mark Abraham]

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