[gmx-users] Hydrogen bonds with version 3.3.1 (fwd)

Gianluca Interlandi gianluca at u.washington.edu
Wed May 3 06:06:04 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,


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