VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Dec 21 2007 - 11:09:10 CST

The origin of this calculation is posted at
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/3943.html.
Please note that the number you're specifying in the autoionize gui is
for total ion concentration (ie, ionic strength when you're using
monovalent ions), *not* concentration of the parent salt. You can keep
electroneutrality working simply by halving the number of cations that
the script wants to add and replacing Na with Mg, but you'll need to
figure out how you want to define the concentration when you're using a
divalent ion. A standardized, more versatile version of autoionize
should be appearing in vmd in the near future, but for now you should be
fine as long as you pay attention to how many ions you're actually adding.
Peter

Lixia Jin Day wrote:
> I am modifying the autoionize.tcl
> the equation to calculate the number of SOD ions:
> set nNa [expr (-$netCharge + 0.0187 * $ionConc * $nWater)/2.0]
>
> can you explain how to get this equation? Thank!
>
>
>
> On Dec 19, 2007 2:37 PM, John Stone <johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu>> wrote:
>
>
> The autoionize.tcl file is actually in the plugins/autoionize...
> directory in the VMD installation on your computer. You can just
> (backup first!) edit that file and change the script to use your
> favorite ion type. Someone else on VMD-L may have already done this
> or have a simpler method, but this was the quickest suggestion that
> came to mind at the time.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu <mailto:vmd_at_ks.uiuc.edu>
>
> On Wed, Dec 19, 2007 at 02:27:04PM -0700, Lixia Jin Day wrote:
> > John,
> > Thank you. I searched the folder and the web, where can I find
> > autoionize.tcl or cionize?
> >
> > Lixia
> >
> > On Dec 19, 2007 1:09 PM, John Stone <johns_at_ks.uiuc.edu
> <mailto:johns_at_ks.uiuc.edu>> wrote:
> >
> > >
> > > Hi,
> > > At present you could either edit the autoionize.tcl script to
> > > use other ion types, or use one of the other ion placement
> tools like
> > > cionize to do this. If you need help, let us know. We'll be
> > > changing the ion placement plugins in VMD to be much more
> flexible
> > > as time goes on...
> > >
> > > Cheers,
> > > John
> > >
> > > On Thu, Dec 13, 2007 at 10:19:06AM -0700, Lixia Jin Day wrote:
> > > > I used autoionize to add NA+ and CL- in the solvent by using
> plugin
> > > > autoionize before. Now I want to add mg2+ ions instead of
> NA+. How can I
> > > do
> > > > this? Thanks!
> > > >
> > > > Lixia
> > >
> > > --
> > > NIH Resource for Macromolecular Modeling and Bioinformatics
> > > Beckman Institute for Advanced Science and Technology
> > > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > > Email: johns_at_ks.uiuc.edu <mailto:johns_at_ks.uiuc.edu>
> Phone: 217-244-3349
> > > WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
> > >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu <mailto:johns_at_ks.uiuc.edu>
> Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/
> <http://www.ks.uiuc.edu/%7Ejohns/> Fax: 217-244-6078
>
>