[gmx-users] Degree of hydrogen bonding

[Justin Lemkul]

On 5/8/14, 11:21 AM, Udaya Dahal 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.
>

The -hbn and -dan options are probably relevant to breaking down what's going 
on.  There are lots of options for g_hbond, read the help description carefully.

-Justin

>
> 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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>
>
>

-- 
==================================================

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

==================================================