VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 06 2010 - 10:16:43 CDT

Hi,
  As Axel pointed out, it appears that the version of autoionize you're
using is doing a bad job in the case of rounding issues. To work around
this you could set the charge of one of your atoms just a little more
negative so it pushes the net charge of the system past -19, which should
cause the code to place the right number of ions. I'll see about addressing
this shortcoming in the code. The original author of this code isn't
actively maintaining it currently, so it falls to us to take care of this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 06, 2010 at 10:49:19AM -0400, Axel Kohlmeyer wrote:
> 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. 

-- 
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