[gmx-users] A few general questions on Gromacs
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jun 25 22:26:47 CEST 2007
Corina Stratan wrote:
>
>
> Dear Gromacs users,
>
> my name is Corina Stratan and I am a Ph.D. student in computer science.
> We have a project in our group in which we try to analyze the behaviour
> of a few typical scientific applications in a cluster environment, and
> we would like to include Gromacs in our tests. We have a few general
> questions about Gromacs, maybe somebody who has experience with it can
> help us:
>
> 1) Which is the typical size of the input/output files for Gromacs
> programs? The ones included in the tutorial are below 50K; are the files
> larger in "real" situations? And if yes, is there any place we can find
> some larger test files?
you can download the benchmark set, in particular the dppc benchmark.
>
> 2) Which would be the typical running time of an mdrun simulation? (or
> put it another way, is the runtime usually significant - i.e., more than
> a few minutes?)
between minutes and years. parallellization helps quite a bit, and with
modern code we scale to hundreds of nodes. however, sometimes on can do
a useful simulation in a couple of minutes and get meaningful (i.e.
publishable) results.
>
> 3) Are the jobs usually run in batch? And if yes, do the batches contain
> a single program, run with different input files, or multiple programs?
>
most often in batch and usually as a single program. sometimes one uses
multiple programs with multiple inputs.
>
> Thank you!
> Corina
>
>
>
> ------------------------------------------------------------------------
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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