[gmx-users] question about g_hbond

[Nidhi Katyal]

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.



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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> ==============================**====================
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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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