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

[bipin singh]

Thanks for the reply.
The difference is almost double, through g_hbond the average number of
contacts are 1821 and through g_mindist it is 3643. The calculation group
does not contains hydrogen atoms.


On Mon, Mar 4, 2013 at 8:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*