[gmx-users] Average no of hbonds

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 6 15:48:56 CEST 2011

Steven Neumann wrote:
> Dear Gromacs Users,
> I am calculating hbonds between my 10 ligands and each residue... How 
> does Gromacs calculate average number of hbonds per timeframe?
> Example:
> for Glycine:
> Av. num of hbonds/timeframe
> 0.96
> To check whether that is correct I added all hbonds formed with Glycine 
> during my simulation time over 2000 (each 50ps) timeframes and I 
> obtained value: 2900. If you divide it by 2000 you will never get 0.96 
> obviously. How does Gromacs calculate it?

Just as you've proposed, the total number of hydrogen bonds divided by the 
number of frames.  Your calculation must have gone awry somewhere.



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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