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

[Erik Marklund]

As Justin implied, -merge could potentially make a factor of 2. Try  
g_hbond -nomerge.

Erik

On Mar 4, 2013, at 4:02 PM, bipin singh wrote:

> 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
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 
>> >
>>
>> ==============================**==========
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>
>
>
> -- 
> *-----------------------
> Thanks and Regards,
> Bipin Singh*
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