[gmx-developers] re: Energy conservation

Charlie Peck charliep at cs.earlham.edu
Sat Apr 8 15:40:07 CEST 2006

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 

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.

charlie peck

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