[gmx-users] Degree of hydrogen bonding

[Mark Abraham]

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,
> Graduate Assistant,
> Department of Physics,
> University of Connecticut
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