[gmx-users] Double counting of h-bonds g_hbond:issue
dahal.udaya at gmail.com
Tue Feb 17 23:14:55 CET 2015
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
>> 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
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> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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