[gmx-users] GROMACS Infrastructure

[Kutzner, Carsten]

Hi Nam Pho,

> On 16. Jan 2019, at 01:40, Nam Pho <npho at uw.edu> wrote:
> 
> Hello GROMACS Users,
> 
> My name is Nam and I support a campus supercomputer for which one of the
> major applications is GROMACS. I was curious if anyone has optimized
> servers for cost and has a blueprint for that,
yes, we did!

We wrote up our experiences in the following publication:

Kutzner, C.; Páll, S.; Fechner, M.; Esztermann, A.; de Groot, B.; Grubmüller, H.: Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), pp. 1990 - 2008 (2015)

A condensed form of the article is available as a webinar:

https://bioexcel.eu/webinar-6-best-bang-for-your-buck-optimizing-cluster-and-simulation-setup-for-gromacs-7-september-2016/

There is also a more recent talk from the last GROMACS developer meeting,
you can download the slides here:

https://www.mpibpc.mpg.de/280063/kutzner04talk-gromacs.pdf

Best,
  Carsten


> what servers and
> configurations are ideal for cost and performance?
> 
> --
> 
> Nam Pho
> 
> Director for Research Computing
> University of Washington
> -- 
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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
http://www.mpibpc.mpg.de/grubmueller/kutzner
http://www.mpibpc.mpg.de/grubmueller/sppexa