[gmx-users] 200 CPU, 3ns/day for 80,000 atoms !!!!

Hannes Loeffler Hannes.Loeffler at stfc.ac.uk
Wed Mar 28 17:56:00 CEST 2012

On Wed, 28 Mar 2012 17:31:47 +0200
Albert <mailmd2011 at gmail.com> wrote:

>   I am using gromacs for membrane simulation (under CHARMM36 FF) which
> contains around 80,000 atoms. I've submitted over 200 CPU in the
> cluster for such system with 2 fs time step. And what really
> astonished is that the efficiency for such simulation is only
> 3ns/day..... I am wondering what happen to my system or gromacs? What
> can I do to fasten the simulation?

In addition to Justin's comment, you could also have a look into
our benchmark reports at
http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx to give you a
feeling for performance.

Scanned by iCritical.

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