[gmx-users] Degree of hydrogen bonding
dahal.udaya at gmail.com
Thu May 8 17:21:14 CEST 2014
Thank you Justin for quick reply. I did exactly what you have mentioned but
the thing is I am getting number of hydrogen bonds per monomer higher than
what i was expecting. Is it possible to see which polymer atom have the
hydrogen bond.( I mean is there a way to see specific atoms using the
indexing so that I can compare the visual image to that number.
On Tue, May 6, 2014 at 10:48 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 5/6/14, 6:05 PM, Udaya Dahal wrote:
>> Hi all,
>> I am simulating a PPO chain in water. I am looking for the degree of
>> hydration. Currently, I am using n=27 monomer CH3-(O-CH(CH3)-CH2)n -O-CH3.
>> I have total 4046 water molecules in a box of 5 5 5.
>> When I use the g_hbond it says it gives the hydrogen bond and the pairs in
>> (0.35nm) distance. As it seems it gives the total hydrogen bonds in the
>> system. I am wondering if there is a way to calculate the total numbers of
>> h-bond between the polymer and the water.
> Yes, if you select your polymer and water as the two groups for analysis,
> this is precisely what you should get. If you select the whole system,
> you'll likely get some ridiculously high number.
> Since I am not familiar with the programming language( reading the huge
>> code is out of question for the time being). The model is the atomistic
>> and and the water i am using is spce. Also how do the boundary bonds are
>> calculated since for a small box, the omission of the boundary bonds will
>> completely alter the property.
> Nearly all Gromacs tools deal with PBC elegantly. g_hbond works fine with
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
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> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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