From: Josh Vermaas (
Date: Tue Mar 11 2014 - 22:00:13 CDT

Hi Adam,

The way I understand the gofr function to work is that there is one
selection that selects the particles that you will be measuring from,
and the second selects the particles you will be measuring to. So if the
first selection was "protein" and the second was "water", you'd be
measuring the gofr for water around the protein. Usually these sorts of
selections are hard to interpret, since lazy selections like I made
above also include buried atoms that may not be close to solution, and
therefore don't contribute until further out in the distribution, and
lead to strange shapes that are difficult to interpret.

-Josh Vermaas

On 03/11/2014 08:03 PM, Adam Goler wrote:
> Hello,
> I'm curious about how this function works. If I understand correctly,
> a simple radial distribution function loops over particles, and counts
> every particle within r +/- dr for all r, where r is increasing radial
> distance (then normalizes).
> What confuses me about the gofr gui plugin is that it allows one to
> choose two selections. How does the recipe change to include the
> second function? Does one merely perform the basic radial distribution
> function calculation with relative displacements?
> Cheers,
> Adam
> --
> Adam Goler
> Graduate Student
> Fulmer 126
> Dept. of Physics and Astronomy
> Washington State University
> PO Box 642814
> Pullman, WA 99164-2814
> Office Phone: (509) 335 7050
> <>