[gmx-users] Hydrogen bonds

Justin Lemkul jalemkul at vt.edu
Sat Jul 4 15:32:04 CEST 2015

On 7/4/15 3:05 AM, Dr. Seema Mishra wrote:
>   Thanks, I will try this option too. But now I would want to look at the particular hydrogen bonds between protein and ligand if these h bonds are present after the simulations. So, please let me know how can I interpret this data that I sent? ---

The index file produced by -hbn is meant to be used with the matrix produced by 
-hbm.  This shows a time series of the breaking and forming of each individual 
hydrogen bond, as listed in the index file from -hbn.


>       On Saturday, 4 July 2015 11:49 AM, soumadwip ghosh <soumadwipghosh at gmail.com> wrote:
>   Hi,
>    the -hbn option in g_hbond in connection to your issue of determining
> the hydrogen bond lifetime or stability does not tell you much. What you
> should be looking at is running the g_hbond with -ac flag which gives you
> the lifetime and H-bond formation energy between two groups specified by
> you in the index file using either a predetermined or the default distance
> and angle cut-off. GROMACS  obeys the Luzar and Chandler description of
> H-bond kinetics which considers the H-bonds labile and the lifetime of the
> same is calculated from the rate constants of H-bond breaking and
> re-forming.
> Cheers,
> Soumadwip


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


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