VMD-L Mailing List
From: Mike Makowski (mmakowsk_at_uci.edu)
Date: Mon Jan 06 2014 - 15:14:21 CST
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.
-- Michael Makowski University of California, Irvine Department of Chemistry, Chemical and Material Physics, Irvine, CA 92617