[gmx-users] High speed performance

Kutzner, Carsten ckutzne at gwdg.de
Mon Aug 3 15:15:03 CEST 2015

Hi Asma,

whether your performance is good/expected depends on some other
parameters you have not mentioned. What time step length do you
use? What electrostatics method? What do you mean by “CPU with
5 nodes?”, I assume you are using 5 MPI ranks on a 40 core CPU?

http://arxiv.org/abs/1507.00898 is a benchmark study with larger
MD systems, however you might find your CPU configuration in one
of the tables and could at least estimate the performance for
your smaller system.


> On 03 Aug 2015, at 15:03, Asmaa El khodary <asma.moh_990 at aucegypt.edu> wrote:
> Hi,
> I'm currently simulating a protein consists of 2776 atoms with 173 residues
> using CPU with 5 nodes, 40 core processors. The performance of the
> simulation is 70 ns per day (50 ns simulation takes almost 18 hours). Is
> this realistic or not?
> Thanks in Advance
> Asma
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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