[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:
> our group at UniRi has been hit by bug 1393 , 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
> 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.
>  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
More information about the gromacs.org_gmx-developers