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

[Justin Lemkul]

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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