[gmx-users] A few general questions on Gromacs

[David van der Spoel]

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
> 
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php


-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++