# [gmx-users] Degree of hydrogen bonding

Udaya Dahal dahal.udaya at gmail.com
Thu May 8 22:24:46 CEST 2014

```Thank you.

On Thu, May 8, 2014 at 12:49 PM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Hi,
>
> Check out g_hbond -h... documentation is written for a reason ;-) You sound
> like you want to see the existence matrix. You might want to create some
> index groups for small parts of your polymer, unless you want to drown
> while interpreting -hbn and -hbm.
>
> Mark
>
>
> On Thu, May 8, 2014 at 5:21 PM, Udaya Dahal <dahal.udaya at gmail.com> wrote:
>
> > 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
> > >> 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
> > >
> > > --
> > > ==================================================
> > >
> > > 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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> >
> >
> > --
> > Udaya Dahal,
> > Department of Physics,
> > University of Connecticut
> > --
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--
Udaya Dahal,