On Thu, 2014-05-15 at 19:09 +0500, sammia khatak wrote:
> HelloI am using sander for energy minimization of protein ligand
> complex but system is running very slow. I am doing this calculation
> on 8 core processor.Is there a way to assign number of processor to be
> used in sander commands.Thanks
See the second chapter of the Amber 14 manual for instructions on how to
compile Amber in parallel using MPI (step 8).
All MPI programs (including Amber) are executed in parallel the same
way. While the exact invocation is somewhat machine-dependent, the
following will generally work:
mpirun -np 8 sander.MPI -O -i mdin -p prmtop -i inpcrd ...
The only differences here are the addition of "mpirun -np 8" (where 8
indicates you run on 8 processors) and the use of sander.MPI instead of
sander.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 15 2014 - 09:00:07 PDT
