[gmx-users] g_hbond

[Nilesh Dhumal]

Thanks.

I will use two groups.

Nilesh
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
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