[gmx-users] Double counting of h-bonds g_hbond:issue
jalemkul at vt.edu
Wed Feb 18 13:41:49 CET 2015
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.
> 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
>>> 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.
>> 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
>> 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
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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
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