[gmx-users] g_hbond

Justin A. Lemkul jalemkul at vt.edu
Wed Aug 31 15:39:55 CEST 2011

Steven Neumann wrote:
> Hi Gromacs Users,
> I have calculated hydrogen bonds and collisions between my ligands and 
> every single residue using g_hbond. Looking at the criteria adpoted by 
> Gromacs I found impossible that number of hydrogen bonds were higher 
> than number of collisions... And what is interesting in one of my 
> residue I obtained result like this... All Hbonds with Glycine - 1872, 
> All Collisions 704.
> Does anyone know how is it possible?

I don't know how any of your numbers are possible (1872 H-bonds forming with a 
glycine?), or what you are defining as a collision and how you calculated it. 
Please provide the exact commands that you're using.  If you're equating a 
contact (e.g. from g_mindist) with a collision, then realize that the default 
criteria for a contact are very different than the geometric criteria for a 
hydrogen bond.



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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