[gmx-users] g_hbond -hbn

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 8 02:37:45 CET 2011

Yao Yao wrote:
> Hi Gmxers,
> I used g_hbond -n protein.ndx -hbn output.xvg
> to get the index of all the atoms forming H-bond with the protein,
> but since H-Bonds should be dynamic as time evolves, I should see 
> changing number of HBonds in the output.xvg which I have not seen yet.
> Kinda confused.

The output of -hbn is an index file, not an .xvg file.  The index file can be 
mapped to the output of -hbm, which is an existence matrix of the hydrogen 
bonds.  Some may swap simultaneously, so you may not see dramatic changes in the 
output of -num (the number of hydrogen bonds).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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