[gmx-users] H-bonds

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 8 13:59:18 CEST 2010

Carla Jamous wrote:
> Hi,
> please I'm trying to measure an hbond between 2 specific atoms. When I 

You won't be able to.  A hydrogen bond is defined as occurring between 3 atoms 
(D-H...A) for geometric reasons, so you have to specify at least three atoms for 
the analysis.

> used g_hbond I didn't the result I expected because it doesn't specify 
> the atoms that constitute the H bond.
> Now I'm trying with g_dist but I encountered a problem: when I do the 
> following in my index file:
> r 172 & a HD2
> it tells me: empty group

Apparently there is no atom named "HD2" in residue 172.  Be sure you're 
analyzing the right residue.


> So please can anyone help me?
> Thank you.
> Carla


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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