VMD-L Mailing List
From: Eduard Schreiner (eduard.schreiner_at_gmail.com)
Date: Mon Jul 12 2010 - 11:08:02 CDT
- Next message: John Stone: "Re: Install VMD on intel i5"
- Previous message: Parisa Akhski: "Autoionize question for DNA molecule"
- In reply to: Parisa Akhski: "Autoionize question for DNA molecule"
- Next in thread: Parisa Akhski: "RE: Cionize question for DNA molecule"
- Reply: Parisa Akhski: "RE: Cionize question for DNA molecule"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
take a look into the cionize plugin:
http://www.ks.uiuc.edu/Research/vmd/plugins/cionize/
eddi
On Mon, Jul 12, 2010 at 10:10 AM, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca> 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.
>
> 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
-- -- ============================================================================= 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 http://www.ks.uiuc.edu/~eschrein/ =============================================================================
- Next message: John Stone: "Re: Install VMD on intel i5"
- Previous message: Parisa Akhski: "Autoionize question for DNA molecule"
- In reply to: Parisa Akhski: "Autoionize question for DNA molecule"
- Next in thread: Parisa Akhski: "RE: Cionize question for DNA molecule"
- Reply: Parisa Akhski: "RE: Cionize question for DNA molecule"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]