[gmx-users] RDF of solvation shell molecules

Justin Lemkul jalemkul at vt.edu
Fri May 23 15:27:51 CEST 2014

On 5/23/14, 12:37 AM, sujithkakkat . wrote:
> Hello Chandan,
>   Thank you for the response.
>    I have used g_rdf, but I guess it gives the RDF for the whole system.
> Say, if I choose water oxygen, it will plot RDF from water molecules in the
> whole system. But, I want the RDF for the solvation shell water molecules
> ,leaving the bulk water . I came across such a plot in an article where the
> author studied the structure of solvation shell . So do you think it is
> possible to do that GROMACS?

You already have it.  The first solvation shell is the first peak in the RDF.



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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