[gmx-users] Average no of hbonds

[Justin A. Lemkul]

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

-- 
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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

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