[gmx-users] H bonds

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 17 02:31:05 CET 2011

larif sofiene wrote:
> Greeting 
> i looking for residues forming Hydrogen bonds with one residue,i can't 
> get that.

Have you tried using an index group that specifies the residue of interest?

> When using -hbm i get an xpm file that contain existence of hbond over 
> time without any indication about who's the other residues.(it is just 
> binary existence)

The index file produced with the -hbn flag maps to the existence matrix in 


> is there a way to get residues engaged in the bond (with occupancy rate 
> if possible)


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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