[gmx-users] segmentation fault message with g_hbond (fwd)
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jan 12 08:51:55 CET 2005
On Tue, 2005-01-11 at 17:56 -0500, Lei Zhou wrote:
> Thanks for the reply. I have been using g_hbond of 3.2.1. Could you tell
> me how to get the source code of the recently modified g_hbond?
Actually it was mainly modified before 3.2.1 but some bugs may have been
fixed in the mean time. Check the CVS instructionson the web site
> ---------- Forwarded message ----------
> Date: Tue, 11 Jan 2005 23:49:20 +0100
> From: David <spoel at xray.bmc.uu.se>
> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] segmentation fault message with g_hbond
> 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 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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