[gmx-users] segmentation fault when using g_hbond

[Erik Marklund]

On Wed, 2006-08-02 at 15:59 +0200, Erik Marklund wrote:
> On Wed, 2006-08-02 at 13:50 +0100, Una Bjarnadottir wrote:
> > Dear users,
> > 
> > I want to use the -sel option in g_hbond and selected three hydrogen 
> > bonds to analyse.  I choose the atom number according to the .gro file 
> > used to make the index file which had the
> >  [ selected atoms]
> > 20 21 24
> > 25 26 29
> > 34 35 37
> > as it says in the manual: Donor Hydrogen Acceptor:  When running the 
> > g_hbond  with the -sel option and chose my group it always comes 
> > segmentation fault but it ran when I didn't use the -sel option and 
> > calculated the number of hydrogen bonds as a function of time. 
> > Is this a bug or is it something wrong with how I made the .ndx file?
> > 
> 
> I think that in recent versions of g_hbond the -sel option does not work
> at all. I don't know if it ever worked. It is a known bug. You will have
> to find another way of doing your analysis or fix the bug yourself, the
> latter being far from trivial I think. 
> 

Furthermore, if you use the -ac, -life or -hbm options I recommend using
the latest version of g_hbond from the cvs repository, since it contains
some bug fixes affecting the reliability of -ac, -life and -hbm output.
It also provides an index file matching the hbm.xpm file when -merge is
used, which wasn't the case in previous versions.

/Erik

> /Erik
> 
> > Best regards, Una Bjarnadottir
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-- 
Erik Marklund, PhD Student, Molecular Biopcysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone: +46 18 471 4537          fax: +46 18 511 755
erikm at xray.bmc.uu.se