From: Parisa Akhski (
Date: Thu Jul 15 2010 - 11:52:54 CDT

Dear Eddi and all VMD users,

It seems that in order to access "Cionize", I have to download the VMD test versions (1.8.8)on BioCoRE page. Unfortunately, I could not find the windows version there. Could anyone please link me to the proper address to download the VMD version that covers "Cionize" in windows?

Thanks in advance,


-----Original Message-----
From: Eduard Schreiner []
Sent: Mon 7/12/2010 12:08 PM
To: Parisa Akhski
Subject: Re: vmd-l: Autoionize question for DNA molecule
take a look into the cionize plugin:


On Mon, Jul 12, 2010 at 10:10 AM, Parisa Akhski
<> wrote:
> Dear all,
> I have been using "Autoionize" in VMD 1.8.7 to neutralize a DNA molecule by
> adding 20 sodium ions. I just figured out that in the "Caveats and
> Limitations" part in the link below, it mentioned that for the systems with
> big electric charge such as DNA (my molecule has 20 negative charges), one
> needs to place ions with regard to the electrostatic potential of the
> molecule since the "Autoionize" is not acceptable in the big electric charge
> cases.
> Does this mean I should add the ions manually? If yes, how do I know there
> is no overlap between the ions and the solvent molecules?
> Thanks for your time,
> Parisa

Eduard Schreiner
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
Phone: 217-244-4361
Fax: 217-244-6078