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

[bipin singh]

Thanks a lot for the suggestions.
It worked.


On Mon, Mar 4, 2013 at 8:44 PM, Erik Marklund <erikm at xray.bmc.uu.se> wrote:

> 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
>>>
>>> --
>>> ==============================****==========
>>>
>>>
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>> --
>> *-----------------------
>> Thanks and Regards,
>> Bipin Singh*
>>
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-- 
*-----------------------
Thanks and Regards,
Bipin Singh*