[gmx-developers] Bug 1393

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 21 09:52:39 CET 2014

On 2014-01-20 16:25, Vedran Miletić wrote:
> Hi,
> our group at UniRi has been hit by bug 1393 [1], which we workaround
> by using 4.6 for genbox and 5.0 git snapshot for other stuff. We are
> still far from publication on this front so 5.0 is an interesting
> experimental toy here.
> Since it is our goal to learn a about GROMACS architecture and
> contribute to its development, I would like to start by trying to fix
> 1393.
> Can anyone with sufficient understanding of the problem provide
> guidance of what has to be done?
What has to be done is indeed a nice challenge to learn development :).
Genbox tries to solvate a protein (or whatever) by placing it in a full 
box of solvent, and the removing the solvent molecules that are too 
close to the protein atoms. In order to do efficient neighborsearching 
the neighborsearching code from mdrun is used. However this is tedious, 
since there are many setup routines involved before one can use the 
inner core of gromacs.

The alternative is the use the special neighborsearching code for 
analysis tools. You can find an example of its use in 
trajectoryanalysis/modules/freevolume.cpp (which I wrote, based on the 
libraries written by Teemu).

> Thanks in advance.
> Regards,
> Vedran
> [1] http://bugzilla.gromacs.org/issues/1393

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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