[gmx-users] Degree of hydrogen bonding

[Udaya Dahal]

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