Date: Tue Jun 28 2011 - 16:05:59 CDT

Hi Axel,

1. Yes, the systems I have been calculating RDFs for are all periodic.

2. The basic differences I've seen so far are not large, however they may
be significant for the analysis I plan on doing. Some of the peak heights
and well depths are slightly different in VMD than in CHARMM (only
different by ~ 0.8 or so), however the most noticeable difference I've
seen so far deals with the convergence of the RDF.

One thing I've observed is that the RDF plateaus at different values in
each program.... for example, when I calculate a specific RDF out to 20
angstroms, in VMD it plateaus at about 0.97 while in CHARMM it plateaus at
approximately 1.06.... this worries me because I'm planning on doing a
Kirkwood-Buff analysis where the convergence of the RDF will have a huge
effect on my results.

Also, I noticed that in CHARMM the RDF tails off once I reach the edge of
my water box... for example, it will plateau at 1.06 up til 18 angstroms
(my box is only 45 A X 38 A X 37 A) and then the RDF will dip down towards
zero the rest of the way.... meanwhile, for the same RDF in VMD it remains
plateaued at 0.97 all the way up to 20 angstroms.... I'm assuming this
just has something to do with the way each program deals with the periodic

I'm also wondering if the sloppiness you mentioned with the normalization
constant may be showing here since my systems are rather small (~
4000-5000 atoms).

Thanks for your help so far,

> 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.
> cheers,
> axel.
>> Best,
>> Tim
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.