[gmx-users] segmentation fault when using g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Wed Aug 2 15:59:13 CEST 2006

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. 


> 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

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