[gmx-users] Degree of hydrogen bonding

[Udaya Dahal]

Hi Abraham,
When I do the indexing, the hbndx gives all h-bonds in ascending order for
all frames and i see the a lot of repeated bonding with the same acceptor
atom. Is it possible to get the index for a particular frame? I see the
option -dt but i didn't quite get that one. Also, the hbnum.xvg file, the
second column represent hydrogen bonds and the third column represents the
pairs within 0.35nm. what does pair represent over here? Does it mean two
h-bonds or donor acceptor number?

Thank you,


On Thu, May 8, 2014 at 4:24 PM, Udaya Dahal <dahal.udaya at gmail.com> wrote:

> 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
>> > >
>> > > ==================================================
>> > > --
>> > > Gromacs Users mailing list
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>> >
>> >
>> >
>> > --
>> > Udaya Dahal,
>> > Graduate Assistant,
>> > Department of Physics,
>> > University of Connecticut
>> > --
>> > Gromacs Users mailing list
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>
>
>
> --
> Udaya Dahal,
> Graduate Assistant,
> Department of Physics,
> University of Connecticut
>



-- 
Udaya Dahal,
Graduate Assistant,
Department of Physics,
University of Connecticut