From: Axel Kohlmeyer (
Date: Tue Jul 06 2010 - 09:49:19 CDT

On Tue, Jul 6, 2010 at 10:16 AM, Parisa Akhski
<> 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?



> Thanks in advance for your help,
> Parisa

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.