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

[Udaya Dahal]

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.

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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