VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Mon Jul 12 2010 - 10:10:11 CDT

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.

http://www.ks.uiuc.edu/Research/vmd/plugins/autoionize/

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