[gmx-users] Average no of hbonds

Mark Abraham Mark.Abraham at anu.edu.au
Tue Sep 6 15:50:08 CEST 2011

On 6/09/2011 11:37 PM, 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?

Presumably by adding up the number in each time frame and dividing by 
the number. Unless you have a highly-exposed glycine, forming more than 
one H-bond seems unlikely, and your 2900 number suggests it's happening 
lots of times. I expect you're comparing a sum of oranges with a sum of 
apples, but without more information about what you're doing in your 
attempt to check, we can't help much. Please be sure to read g_hbond -h, 
and the legends of any .xvg files you're looking at.


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