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.
Mark
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