[gmx-users] g_hbond

[Nilesh Dhumal]

>
>
> 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)
>
>> 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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