[gmx-users] Double counting of h-bonds g_hbond:issue

[Justin Lemkul]

On 2/17/15 5:14 PM, Udaya Dahal wrote:
> Thanks Justin for prompt reply. Actually I calculated for the h_bonds with
> same criteria for (angle 30 and distance(D-A) 0.35nm) from VMD, and the
> number is lot less for both Polymer water and water water.  I have 193
> water molecules and the H-bond from VMD with same criteria gives me 232
> H-bonds while GROMACS provides 340.  The value GROMACS provides is better
> in the sense that it matches more closely to the experimental value but I
> kind of unsure since the visualization (in VMD ) also showed very few bonds.
>   It shows like only 5 bonds from vmd calculation(and visualization) in
> previously mentioned Polymer water h-bonds.
>

Probably VMD's plugin and g_hbond are doing something different.  Note the VMD 
documentation seems to indicate the angle criteria is defined differently (D-H-A 
angle whereas g_hbond uses H-D-A, yet they use a similar value as a cutoff). 
Define a very small test system, something that you can literally look at and 
know the answer for sure, and see if the two programs agree.

-Justin

> On Tue, Feb 17, 2015 at 7:58 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/16/15 7:39 PM, Udaya Dahal wrote:
>>
>>> Hi All,
>>>
>>> When I used the g_hbond the hydrogen bonding i was getting was quite good
>>> but when I checked the index file i find double counting of the bonds. So
>>> far, it seems to me that g_hbond is giving higher than the real hydrogen
>>> bonds present in the system. For eg. in the following OW-HW-oxygen, we see
>>> there are two bonds between 109(OW) and 110(HW) for two different polymer
>>> oxygens.
>>>
>>> Can anyone explain this issue?
>>>
>>>        76     77     12
>>>       100    101     47
>>>       109    110     40------->1 (same hydrogen with two different oxygens)
>>>       109    110     54------->2(same hydrogen with two different oxygens)
>>>
>>
>> So does a visual inspection of this particular frame confirm that there
>> shouldn't actually be hydrogen bonds with these atoms?  This isn't
>> double-counting, it's just a bit unusual, but is possible within the
>> context of whatever criteria you have set for defining a hydrogen bond.
>>
>> -Justin
>>
>>        211    212     54
>>>       211    212     68
>>>       337    338     68
>>>       343    344      5
>>>       343    344     19
>>>       403    404     61
>>>       487    488      5
>>>       511    512     26
>>>       511    512     40
>>>       538    539     33
>>>       592    593     12
>>>       592    593     26
>>>
>>> Hbnum.xvg shows
>>> hydrogen bonds             pairs within 0.35
>>> 16                                       8
>>>
>>>
>>> Regards,
>>> Udaya
>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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