[gmx-users] RDF

[Justin Lemkul]

On 5/18/15 2:55 AM, mah maz wrote:
> Hi Justin
> The fact is I want to calculate water density in the system. If I select
> group1: oxygen and group2: oxygen, g_rdf command gives me very large
> numbers. Is it the number of atoms that should be changed to g/cm3?
> Besides, what does it calculate, each O is a reference atom during
> calculation?

All of this is in the manual.  The value of the RDF is the relative probability 
of finding a given particle as a function of distance.  If you just want 
density, there's a separate tool for that, conveniently called "g_density."

-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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