Thanks Erik, In case I run my simulations on 4 nodes, please let me know what do I have to add to the command to start "MPI"? I have used the commands: *grompp -f NVT_50ns.mdp -o NVT_50ns.tpr -c NVT_20ns.g96 -p topol.top mdrun -s NVT_50ns -o NVT_50ns -c NVT_50ns -x NVT_50ns -e NVT_50ns -g NVT_50ns -v* however, the speed was still the same. Best regards,
Cuong 2012/3/15 Erik Marklund <[email protected]> > If you are to run on a single node, then there's no need for mpi nowadays. > mdrun uses all cores it can find anyway. If you need to split your > calculation over many machines, however, you will need mpi. > > Best, > > Erik > > 15 mar 2012 kl. 04.50 skrev cuong nguyen: > > Dear Gromacs users, > > I prepare to run my simulations on the supercomputer on single node with > 64 CPUs. Although I have seen on Gromacs Mannual suggesting to use MPI to > parellel, I still haven't understood how to use this application and which > commands I have to use. Please help me to deal with this? > > Many thanks and regards, > > Cuong > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > ----------------------------------------------- > Erik Marklund, PhD > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 6688 fax: +46 18 511 755 > [email protected] > http://www2.icm.uu.se/molbio/elflab/index.html > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Nguyen Van Cuong PhD student - Curtin University of Technology Mobile: (+61) 452213981
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