[gmx-users] question about g_hbond

[Justin Lemkul]

On 9/1/13 1:30 PM, Nidhi Katyal wrote:
> 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
>

Try 4.6.3.  If it still doesn't work, you can feel free to file a bug report on 
redmine.gromacs.org, or otherwise just use the g_mindist output.

-Justin

>
> 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
>>>>>>
>>>>>> --
>>>>>> ==============================******====================
>>>>>>
>>>>>>
>>>>>>
>>>>>> 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 <jalemkul at outerbanks.**umaryland.edu<jalemkul at outerbanks.umaryland.edu>>>
>>>>>> |
>>>>>> (410) 706-7441
>>>>>>
>>>>>> ==============================******====================
>>>>>>
>>>>>>
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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 <jalemkul at outerbanks.umaryland.edu>> |
>>>> (410) 706-7441
>>>>
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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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-- 
==================================================

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 | (410) 706-7441

==================================================