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