jalemkul at vt.edu
Sun May 17 15:15:19 CEST 2015
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 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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