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! Arden On Tue, Apr 20, 2010 at 7:55 AM, Hsin-Lin <jian...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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