[gmx-users] question about g_hbond

[Nidhi Katyal]

I have created my files long time ago using version 4.0.7. But now
analyzing the same files using g_hbond/g_mindist using version 4.5.5


On Sun, Sep 1, 2013 at 10:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/1/13 1:17 PM, Nidhi Katyal wrote:
>
>> Even after giving same cutoff radius of 0.35nm in both, I am getting
>> around
>> 400 contacts per timeframe with mindist but 0 contacts with g_hbond.
>>
>>
> What version of Gromacs are you using?
>
> -Justin
>
>
>>
>> On Sun, Sep 1, 2013 at 10:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 9/1/13 1:08 PM, Nidhi Katyal wrote:
>>>
>>>  The two groups are:  protein and cosolvent molecules. With g_mindist
>>>> -on ,
>>>> I am getting values of around 6500 per timeframe. But then why g_hbond
>>>> giving different results.
>>>>
>>>>
>>>>  Are you using the same cutoff radius for both?
>>>
>>> -Justin
>>>
>>>
>>>  On Sun, Sep 1, 2013 at 10:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 9/1/13 12:50 PM, Nidhi Katyal wrote:
>>>>>
>>>>>   Hello,
>>>>>
>>>>>> I would like to calculate number of contacts between two groups, for
>>>>>> which
>>>>>> I am using following command:
>>>>>> g_hbond -f *.xtc -s *.tpr -num *.xvg -contact -b 49000 -e 50000
>>>>>> I am getting 0 as the output. But when I am calculating number of
>>>>>> hydrogen
>>>>>> bonds between the same two groups by using the above command without
>>>>>> contact option I  am getting 5.2 as the output.
>>>>>> My question is wouldn't number of contacts be higher than number of
>>>>>> hydrogen bonds since hydrogen bonds are subset of contacts.
>>>>>>
>>>>>>
>>>>>>  In theory, but something might be failing.  What are the groups you
>>>>> are
>>>>> choosing?  What is your expected outcome?  What does the output of
>>>>> g_mindist -on give you?
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==============================******====================
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>>>>> Justin A. Lemkul, Ph.D.
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>>> Justin A. Lemkul, Ph.D.
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>>> University of Maryland, Baltimore
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> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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