From: Adam Goler (adamgoler_at_gmail.com)
Date: Tue Mar 11 2014 - 23:55:56 CDT

Josh,

So does the function ignore all atoms that are not part of the selection
for the purposes of calculation?

Is the radial pair distribution function determined by counting the number
of atoms within a spherical shell as the radius increases from the location
of selection 1 to selection 2?

Thanks,
Adam

On Tue, Mar 11, 2014 at 8:00 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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
>
> adamgoler.com
>
>
>

-- 
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
adamgoler.com