[gmx-users] Calculate RDF within a certain distance from atom

[Justin Lemkul]

On 2/20/18 11:53 AM, Dilip H N wrote:
> Hello,
> How to get RDF within a certain distance..??
>
> Say for eg., i have glycine amino-acid and i want the RDF of Oxygen water
> atoms within 0.7nm of C-alpha (Calpha-Ow).
>
> how can i get it from in-house gmx rdf command...??

What do you hope to achieve from such a metric? RDF has to be normalized 
against bulk occupancy, which will of course not be achieved at a 0.7-nm 
distance. If you are interested in certain properties within given 
solvation shells, distances, etc. compute the normal RDF so that it is 
properly normalized and interpret the outcome of that calculation.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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