VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 06 2010 - 09:49:19 CDT

On Tue, Jul 6, 2010 at 10:16 AM, Parisa Akhski
<Parisa.Akhshi_at_chem.queensu.ca> wrote:
>
> Dear VMD users,
>
> I am using autoionize to neutralize a DNA molecule. I am using the command
> below as posted on the VMD mailing list to make it only place enough ions to
> neutralize the system:
>
> autoionize -psf file.psf -pdb file.pdb -is 0.0001
>
> The system net charge before adding ions is -18.9999991446e and after adding
> ions is -0.999999144592e. Isn't that supposed to be zero after adding ions?

that looks very much as if the autoionize code doesn't
handle rounding errors very well. i suggest you contact
the author.

> Or is it acceptable?

no.

cheers,
    axel.

> Thanks in advance for your help,
>
> Parisa
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.