[gmx-users] Hydrogen bonds with version 3.3.1

Gianluca Interlandi gianluca at u.washington.edu
Tue May 2 09:57:42 CEST 2006

Dear David,

Thanks for your reply,

> The hbond program is rather complex, but the hbond criterion itself is not
> (but note that the definition of the angle has changed from 3.2.1 to 3.3, from
> AHD to ADH).

This hasn't been clear to me as the online documentation says DHA:

-a  real  30  Cutoff angle (degrees, Donor - Hydrogen - Acceptor)

> Maybe you should start by removing the options:
> -nonitacc -hbm  -hbn -nomerge

Do these options influence the way hydrogen bonds are calculated?

I want to know which hydrogen bond is formed in each frame. For this 
reason I need "-hbm" which gives me a matrix. However, in order to know 
what atoms correspond to the index in the y-axis of the matrix "hbmap.xpm" 
I need "-hbn". Finally, I also need "-nomerge" because the index file 
"hbond.ndx" inlcudes even those hydrogen bonds which are merged, and thus 
the number of hbonds in "hbond.ndx" would not correspond to the number of 
hbonds in "hbmap.xpm". But maybe there is an easier way to do this.



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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