VMD-L Mailing List

From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Sun Jan 16 2005 - 12:14:04 CST

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