[gmx-users] RDF

[Justin Lemkul]

On 5/17/15 5:47 AM, mah maz wrote:
> Dear all,
> I want to calculate the radial distribution function of water molecules in
> my system. I use g_rdf -f traj.xtc -n -o. It gives me large numbers which
> is not logical I suppose. Is it meaningful if I separate oxygen and
> hydrogen atoms in the index file and calculate the RDF for O-O atoms? Is
> reference atom necessary to get RDF?

RDF is always calculated relative to a reference, but the default behavior is to 
consider all atom pairs; see the manual.  It is generally standard practice in 
liquid RDF to separate out O-O vs. H-H etc.  There is even an example figure of 
this in the manual.

-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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