[gmx-users] g_hbond -hbn

[Justin A. Lemkul]

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================