[gmx-users] parallel simulation in dual core PC

Arden Perkins perkina2 at eou.edu
Wed Apr 21 19:12:29 CEST 2010

Did you preprocess the .tpr file for 2 cores with grompp? Also, I believe
you have to have an additional -np 2 after the mdrun_mpi command: mpirun -np
2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
-c 200ns.gro -np 2
-- at least this is what I understand from what my prof told me. We just
started running parallel simulations for an undergraduate research project
and I believe that is how we input commands. I'm sure the gromacs experts
will correct me if I'm wrong.

Good luck!

On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin <jiangsl at phys.sinica.edu.tw>wrote:

> Hi,
> I want to use my dual core PC to do the simulation.
> The version of GROMACS installed is version 4.0.5.
> According the message post by others on mailing list before.
> I type "lamboot" first, and type the commend:
> mpirun -np 2 mdrun_mpi -s 200ns.tpr -e 200ns.edr -o 200ns.trr -g 200ns.log
> -c 200ns.gro.
> When the simulation starts, I use the commend, "top", to check the utility
> of CPU.
> I found there is only one core which is used by GROMACS.
> And the utility of this core is separated to 52% and 48% for two mdrun_mpi
> jobs.
> How can I do for that?
> Any and all assistance is greatly appreciated.
> Hsin-Lin
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