[gmx-users] find hbond between different groups during simulation

[Justin Lemkul]

On 1/20/16 4:08 AM, Mahboobe Sadr wrote:
> Dear all,
>
> I want to find hydrogen bonds between waters and The protein. since in each
> frame I selected some specifc waters, I want to find hydrogen bonds during
> simulation for different waters(which are in the pore of the protein) and
> the protein.
>   as  "g_hbond" doesn't any option like "-select" in "gmx distance", I
> couldn't find the hbond i want.
>

Use gmx select to get per-frame index groups that satisfy the selection 
criteria, then run the analysis frame by frame.

-Justin

-- 
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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

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