[gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond

bipin singh bipinelmat at gmail.com
Tue Oct 23 17:41:47 CEST 2012

Hello all,

I was trying to calculate solvent mediated H-bond between a amino acid
residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after
creating separate index) with the help of g_hbond version 4.5.3. But I am
getting segmentation fault while running g_hbond. Moreover I am getting
error only for this particular residue, whereas with other residues the
samilar calculation is working fine.
I have used the following command for the calculation:

g_hbond -f traj.xtc -s md.tpr -num hbnum.xvg -hbn hbond.ndx -g hbond.log
-dist hbdist.xvg -hbm hbmap.xvg -n index.ndx

Please provide your suggestions to rectify the error.

*Thanks and Regards,*
Bipin Singh

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