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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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