VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 06 2014 - 16:23:10 CST

On Mon, Jan 6, 2014 at 4:14 PM, Mike Makowski <mmakowsk_at_uci.edu> wrote:
> Hello all,
>
> I have a question that is similar to one posted back in 2011 regarding the
> normalization of the radial distribution function. I'm looking at a number
> of binary solutions with different concentrations. The box for each solution
> is 38 x 38 x 140 and contains between 5000 and 8000 atoms depending on the
> concentration. When I run the RDF utility for these solutions, each one
> converges to a different value. What's more is that they are converging at
> values much higher than one. It appears that the trend is following the
> number density of the solution but when I try to normalize accordingly, it
> doesn't seem to correct the problem adequately.
>
> Some more information:
>
> 1. I'm aware that the type of selections are important. Each of the RDFs
> that I am concerned with are those that sel1 = sel2.
>
> 2. The box has periodic boundary conditions but have tested the result
> without PBC checked in the utility and it doesn't resolve the issue.
>
> 3. The max r that I'm using is smaller than half the width of my box. I'm
> using the default r = 10 A. Changing this value along with the histogram bin
> size doesn't seem to correct this problem either.
>
> I'm really just searching for the proper way to normalize these RDFs such
> that they all converge to one. Can anyone help me with this problem? Thanks
> for your time and consideration.

mike,

two things:

- can you provide some example data and example g(r) plots (with
description of the choice of parameters)?
- can try with the latest alpha test version (instructions are at:
http://www.ks.uiuc.edu/Research/vmd/alpha/) to make sure you have all
known bugfixes?

you can use the biocore biofs for the VMD public project you store
your example data (please create a subdirectory), so you won't have to
worry about attachments and flooding the mailboxes of many users with
content that they don't care about.

axel.

>
> Regards,
> Mike Makowski
>
> --
> Michael Makowski
> University of California, Irvine
> Department of Chemistry,
> Chemical and Material Physics,
> Irvine, CA 92617
>
> 

-- 
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.