VMD-L Mailing List

From: Adam Goler (adamgoler_at_gmail.com)
Date: Wed Mar 12 2014 - 13:02:04 CDT

Axel,

Thanks for the info (and the reference). I think I should be able to figure
it out.

Adam

On Tue, Mar 11, 2014 at 10:35 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> adam,
>
> before speculating and guessing too much, i would recommend, you look
> up the proper definition in a statistical mechanics or MD simulation
> or simple liquids text book. in short, the radial distribution
> function is the "relative" probability to find an atom of type b at a
> given distance from an atom of type a. both types can be the same,
> different or overlap. an ideal gas gives an g(r) that is 1.
>
> in practice, you loop over all atoms in the first group and then
> create a distance histogram of all atoms in the second group (which
> can be identical). the GPU accelerated implementation in VMD has some
> additional tricks and gimmicks and they are explained in this
> publication:
>
> Fast Analysis of Molecular Dynamics Trajectories with Graphics
> Processing Units: Radial Distribution Function Histogramming, B.G.
> Levine, J.E. Stone, A. Kohlmeyer, J. Comput. Phys. 230(9), 3556-3569
> (2011)
>
> HTH,
> axel.
>
> On Wed, Mar 12, 2014 at 12:55 AM, Adam Goler <adamgoler_at_gmail.com> wrote:
> > 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
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
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