[gmx-users] Difference in Number of contacts through g_hbond and g_mindist

[Justin Lemkul]

On 3/4/13 9:08 AM, bipin singh wrote:
> Hi All,
>
> I have a doubt regarding the calculation of number of contacts between two
> groups. Because, I am getting different number of contacts calculated
> through g_hbond -contact option and g_mindist -on option.
> I have used same cutoff for distance (0.6nm) in both the cases.
>

How different are the results?  The g_hbond code is very complex, but you'd 
probably have to go into the inner workings of both programs to understand why. 
  I also do not know whether other settings in g_hbond will matter, like -merge, 
or whether or not g_hbond will only calculate contacts among H-bond 
participating groups.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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