[gmx-users] segmentation fault message with g_hbond

[David]

On Tue, 2005-01-11 at 16:56 -0500, Lei Zhou wrote:
> Dear GMX users,
> 
> I have been trying to use g_hbond to analyze the existence of 
> hbonds at each frame (-hbm). But I always get a error message of 
> segmentation fault and could not get the xpm file output. Is the 
> selection index input file (-sel) essential for the output of xpm file?
> I could get the normal xvg output (-num) with -nomerge flag setup.
> 
> Here is the script I used and the screen print out:
> 
> g_hbond -nomerge -f md.trr -n md.ndx -s md.tpr -g test.log -hbn 
> test.ndx -hbm test.hbm
> 
> Checking for overlap...
> Calculating hydrogen bonds between two groups of 8636 and 100 atoms
> Found 1244 donors and 2376 acceptors in group 'A'
> Found 8 donors and 44 acceptors in group 'B'
> Going to allocate 71011 kb of memory,  and that's only the beginning
> trn version: GMX_trn_file (single precision)
> Reading frame       1 time 10001.000
> Will do grid-seach on 23x23x17 grid, rcut=0.35
> Last frame         50 time 10050.000
> Found 29 different hydrogen bonds in trajectory
> 
> Back Off! I just backed up hbnum.xvg to ./#hbnum.xvg.5#
> Average number of hbonds per timeframe 6.940 out of 36872 possible
> Segmentation fault
> 
> Any help will be appreciated.
Sounds like a bug. This part of g_hbond has been rewritten recently.
> 
> Sincerely,
> 
> Lei Zhou
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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