[gmx-users] segmentation fault using g_hbond

Joern Lenz JLenz at zbh.uni-hamburg.de
Thu Feb 8 17:09:10 CET 2007

Dear Gromacs guys and users,
some days ago I posted the question below to the forum but unfortunately got 
no answer yet. I do not want to get on your nerves but perhaps you overread 
it and are now able to answer the it.

Thank you very very much in advance and greetings

----------  Forwarded Message  ----------

Subject: segementation fault using g_hbond
Date: Wednesday 07 February 2007 10:08
From: Joern Lenz <JLenz at zbh.uni-hamburg.de>
To: gmx-users at gromacs.org

Dear Gromacs users,

i have simulated a protein-dan-complex in water and now i am doing the
analyzing of my runs.
everything is fine except a mistake occuring when using g_hbond.

this is the command i am using:
g_hbond -f blah.pdb -s blah.tpr -n blah.ndx -num blah_num.xvg -ac blah_ac.xvg
-ang blah_ang.xvg -don blah_don.xvg -nhbdist blah_nhbdist.xvg

and the error message is:
Found 678 donors and 1684 acceptors
Reading frame       0 time    1.000
Will do grid-seach on 31x31x31 grid, rcut=0.35
 '', 293160 atoms
Last frame          0 time    1.000
Found 13 different hydrogen bonds in trajectory
Found 9 different atom-pairs within hydrogen bonding distance
Merging hbonds with Acceptor and Donor swapped
- Reduced number of hbonds from 13 to 13
- Reduced number of distances from 9 to 9
Average number of hbonds per timeframe 13.000 out of 570876 possible
ACF 13/13
Normalization for c(t) = inf for gh(t) = inf
Segmentation fault

Can anyone tell me what is going wrong here ?
Thanks very much for answers.
a nice day to all of you
Greeting Joern


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