[gmx-users] question about g_hbond
jalemkul at vt.edu
Sun Sep 1 19:10:10 CEST 2013
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?
> 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:
>>> 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 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.
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
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