[gmx-users] Time evolution of distance of Hydrogen bond

Justin Lemkul jalemkul at vt.edu
Thu Aug 21 03:09:43 CEST 2014

On 8/20/14, 8:54 PM, MUSYOKA THOMMAS wrote:
> Dear Users,
> I am working on protein-ligand MD simulation. I have managed to get the
> number of H-bonds formed between the protein and ligand throughout my
> simulation period. I noticed three important residue participate in the
> formation of this H-bonding network.
> I need to determine the *time evolution* of the specific H-bond *distance*
> throughout my simulation. How do I go about this?

Distances are measured with g_dist/gmx distance.  Create index groups for each 
of the heavy atoms that participate as donor and acceptor and measure the 
distance between each relevant pair.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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