[gmx-users] Degree of hydrogen bonding

[Justin Lemkul]

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 one
> 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 PBC.

-Justin

-- 
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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 601
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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