Re: [gmx-users] mdrun in parallel

grompp -np 16 On 11/21/08 7:06 PM, [EMAIL PROTECTED] wrote: Hi All, I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in parallel using the command: mpirun -machinefile /storage1/home/rgr/machines_16 -np 16 /storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -

Re: [gmx-users] mdrun in parallel

Hi Alessandro, With gromacs versions <4 you have to generate the .tpr file with grompp using the flag -np 16 to be able to run on 16 processors. But why not upgrade to gromacs 4.02 and get much better scaling? Cheers, Tsjerk On Fri, Nov 21, 2008 at 12:06 PM, <[EMAIL PROTECTED]> wrote: > Hi All

[gmx-users] mdrun in parallel

Hi All, I'd need an help to run GROMACS 3.3.3 in parallel. I'm running mdrun in parallel using the command: mpirun -machinefile /storage1/home/rgr/machines_16 -np 16 /storage2/rgr/software/gromacs/bin/mdrun_d -s min0.tpr -g min0.log -e min0.edr -o min0.trr -x min0.xtc -c min0.gro but the followi