From: Axel Kohlmeyer (
Date: Tue Jun 28 2011 - 13:06:49 CDT

On Tue, Jun 28, 2011 at 1:34 PM, <> wrote:
> Hello all,

hello tim,

> I was wondering if someone could tell me how RDFs are normalized when
> using the gofr plugin in VMD.  I'm specifically interested in what bulk

are we talking periodic systems here?

> density is used for normalization.  I've been using VMD to calculate RDFs

the total particle density of the two selections
periodic systems. for non-periodic input, the
normalization is not well defined and a number
density of 300K bulk water is arbitrarily picked.

> and I've noticed some differences between the RDFs generated by VMD when

which differences?

> compared to those generated by other software.  I'm not sure why that is,
> so I'm looking to see if the normalization is done differently in VMD when
> compared to other software programs.  Thanks in advance for any help.

the question is really how large differences we are looking at.
many RDF tools are somewhat sloppy in how to compute
the normalization constant and don't account for finite size
effects. this usually doesn't show unless you have a rather
small number of atoms in your system.


> Best,
> Tim

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.