VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Apr 02 2009 - 09:25:33 CDT

On Thu, 2009-04-02 at 15:50 +0200, Kalavera_at_gmx.net wrote:
> hello everybody,
> after using the autoionize script from Ilya Balabin and Marcos Sotomayor
> (http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/)and exchanging the sodium with potassium I got confused by the visual results in VMD, because of different radii for potassium and chloride ions.
> In my case the chloride ion is displayed nearly two times smaller than the potassium if VDW is used as the drawing method. I need to know if this is the normal case and whether my system is setup properly.

unless you use a file format that contains explicit radii,
VDW uses covalent radii from an internal table. those have
no idea that you have ions. in general, you have to keep in
mind that VMD knows only what is provided. it deliberately
does not know any chemistry.

cheers,
  axel.

> Thx for your replies,
> M.Kalavera 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.