[gmx-developers] re: Energy conservation

David van der Spoel spoel at xray.bmc.uu.se
Sat Apr 8 16:00:46 CEST 2006

Charlie Peck wrote:
> On Apr 7, 2006, at 3:09 PM, Michael Shirts wrote:
>>> We have similar results for
>>> proteins with H-bonds constrained (using SHAKE) in water clusters, in
>>> vacuum, but much shorter simulations.
>> It might be good to have a validation data, test cases in the CVS.   I
>> think one of the problems is that we say "I've checked this" but if
>> the data and the mdp's used to generate the data is not easily
>> acessible, we end up talking past each other.  Might this be a feature
>> other people are interested in?  I think it would make things easier.
> I'm neither a physicist or a chemist, rather a computer scientist who 
> has worked a little bit with the GROMACS codeline.  From my experience 
> having test cases in CVS such as Michael described would be very helpful.
> The students I work with have some experience with developing automated 
> test harnesses for other scientific cores, if someone can provide us 
> with the data, mdp files, command lines, etc. to use we could put 
> something together.

You can checkout the test suite using
cvs co tests

This test suite is incomplete, and some tests are known to fail because 
of heaps of bug fixes since we did the reference calculations, i.e. it 
is out of date as well. Another set of tests is formed by the Pande 
group's AMBER port (http://folding.stanford.edu/ffamber).

> charlie peck
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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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