VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 21 2005 - 17:30:29 CST

Hi,
  I'd suggest that you contact Ilya Balabin about this detailed
question, he is the author of the autoionize plugin:
  http://www.chem.duke.edu/~ilya/
  http://fds.duke.edu/db/aas/Chemistry/post%2520docs/ilya.balabin

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Jan 16, 2005 at 01:14:04PM -0500, Blake Charlebois wrote:
> Hello everyone,
>
> I have been experimenting with the VMD Autoionize plugin and the SODIUM
> program. I one question about each.
>
> AUTOIONIZE QUESTION:
> For the Autoionize "is" parameter, it seems that the user specifies target
> osmolarity and Autoionize computes the number of Na or Cl ions to add using
> the following formula:
>
> (Na ions added + Cl ions added) =
> (0.0187) x (target osmolarity) x
> (number of water molecules in
> system before ion addition)
>
> I would have expected 0.01807 (molar mass over density for pure water) or
> 0.0183 (molar mass over density for TIP3P water). Does anyone know how they
> arrived at 0.0187?
>
>
> SODIUM QUESTION:
> I have a protein with charge -13. Suppose I want to add x Na ions and (x-13)
> Cl ions using SODIUM. I could add...
> A) x Na, followed by (x-13) Cl
> B) 1 Na, followed by 1 Cl, followed by 1 Na, etc.
> C) x/4 Na, (x-13)/4 Cl, x/4 Na, etc.
>
> I expect approaches B and C would provide more reasonable results. On the
> other hand, the water and ions should be equilibrated for a long time (>1
> ns?) with the protein fixed to refine ion placements regardless, so perhaps
> the initial coordinates do not need to be selected too carefully. Does
> anyone have an opinion on this?
>
>
> Thank you,
> Blake Charlebois 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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