[gmx-users] g_hbond

[Justin Lemkul]

On 7/9/15 9:13 PM, Nilesh Dhumal wrote:
>>
>>
>> On 7/9/15 9:02 PM, Nilesh Dhumal wrote:
>>> Hello,
>>>
>>> I am calculating g_hbond for water system.  I have a question about
>>> specifying two group for calculating hydrogen bond.
>>>
>>> Do I specify atoms in triplet(O-H---O)?
>>> Can I specify O-H as one group (Donor-Hydrogen) and O in other group
>>> (Acceptor)?
>>
>> If the system is pure water, you do not need any special index groups.
>
> I have DMSO in the system. I just mentioned water to make it simple.
> I am interested in O--H---O(DMSO) interactions?
>
> How should I specify this?
>
> With one triplet O--H---O(DMSO) or two groups one O--H and second O(DMSO)

The latter - just use DMSO and water groups.  O can be a donor or acceptor, and 
g_hbond intelligently figures out whether or not a given atom is a donor or 
acceptor (or both).

-Justin

>>
>>> Default  -r cutoff is 0.35nm. Is the distance between
>>> hydrogen---acceptor
>>> or distance between donor---acceptor?
>>
>> Read the first sentence of the help description.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> 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 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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