[gmx-users] segmentation fault message with g_hbond

Lei Zhou lz150 at columbia.edu
Tue Jan 11 22:56:59 CET 2005

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.


Lei Zhou

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