From: Axel Kohlmeyer (
Date: Thu Jan 19 2012 - 21:12:49 CST

On Jan 19, 2012, at 10:03 PM, "Zumot, Elia Nabil" <> wrote:

> Dear VMDers,
> Any reason why VMD shows sodium ions to be bigger than chloride when it should be the other way around?
> In crystals the radius of Na+ is 0.095 nm and that of Cl- 0.181 nm.

That is because VMD cannot tell the difference between an element and
an ion or a chlorine or chloride and a carbon.

If you don't like VMD's choices you can always write a little script
that changes it or use a file format that does contain the radius
information in a way that VMD supports reading it.

VMD is very deliberately a very dumb and ignorant software that relies
on you to provide it with the proper information. It does not even try
to be smart (for the most part, that is).


> Thanks
> Elia Zomot
> Elia Zomot, PhD
> Computational and Systems Biology Department
> School of Medicine, University of Pittsburgh
> 3083 BST3, 3501 Fifth Ave, Pittsburgh, PA 15213
> Voice: 412 624 8699 - Fax: 412 648 3163