[gmx-users] large scale simulation?

Szilárd Páll szilard.pall at cbr.su.se
Sat Mar 31 03:56:03 CEST 2012

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.


On Fri, Mar 30, 2012 at 7:02 PM, Albert <mailmd2011 at gmail.com> 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.
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