[gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi gianluca at u.washington.edu
Thu May 4 21:00:54 CEST 2006

> But now for the most important question: is there a reproducible problem 
> with the angle?

Yes. I include everything into a tar:


I'm using the following command to verify if the hydrogen bond "ARG 552
HH12 - GLN 548 OE1" is formed along the trajectory:

g_hbond -f trajectory.trr -s topol.tpr -r 0.27 -a 60 -n select.ndx -noda
-nonitacc -hbm -hbn -nomerge

File "hbmap.xpm" tells me that the hbond is formed in only three frames.
However, if I plot the distance with g_dist and the angle with g_angle as
a function of time (see dist.xvg and angaver.xvg) the distance between
hydrogen and acceptor is below 0.27 nm in 61% of the frames and the angle
(ADH) is below 60 degrees in almost all frames. All used commands are in
the file "commands".

Thanks a lot for your help,


Dr. Gianluca Interlandi gianluca at u.washington.edu
                    +1 (206) 685 4432
                    +1 (206) 714 4303

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.

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