[gmx-users] Calculate RDF within a certain distance from atom
Justin Lemkul
jalemkul at vt.edu
Tue Feb 20 18:28:25 CET 2018
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.
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Virginia Tech Department of Biochemistry
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