On a single quad 16-core Interlagos node with system size 34k atoms I get 55-60 ns/day and even with 24k atoms ~70 ns/day (solvated protein amber99 + tip3p) . On three of these nodes I think you can get close to 100 ns/day, but it will be close to the scaling limit.
Have you considered vsites with larger timesteps? Additionally, the new cut-off scheme which will come in 4.6 you can get better scaling due to the more even nonbonded workload. -- Szilárd On Fri, Mar 30, 2012 at 7:02 PM, Albert <[email protected]> wrote: > Hello: > > I am wondering does anybody have experience with GROMACS for large scale > simulation? I've heard lot of people said that it would be difficult for > Gromacs to do so. eg: I've got a 60,000 atoms system, is it possible for > GROMACS to produce 100 ns/days or even more? suppose I can use as much CPU > as possible.... My recent experience for such system, Gromacs can only > produce up to 20ns/day.... If I would like to produce 1000 ns, I have to > wait for 50 days...... > > thank you very much > > best > A. > > -- > 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 -- 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
