[gmx-users] RDF analysis with respect to center of mass of Protein

[Justin Lemkul]

On 9/18/14 2:04 PM, Carlos Navarro Retamal wrote:
>
> Dear gromacs users,
> In order to measure the interactions between a Protein with respect to a mixture solvent solution  (glycerol-water) i’m trying to measure the RDF between the protein with respect to the C and O atoms of Glycerol respectively.
> By now i have measured g(r) between:
>
> Protein - Glycerol
> Protein Backbone - Glycerol
> SideChain - Glycerol
>
> but sadly, because i’m considering a huge amount of atoms of the Protein, the RDF graphic doesn’t look that good.
> On that way i thought that maybe a better approximation will be to measure the RDF between the center of Mass of the protein with respect to the glycerol molecules, but i don’t know how to use make_ndx to create such kind of group.

It's not a task for make_ndx.  g_rdf does this with the -com option.

-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 601
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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