From: Blake Charlebois (
Date: Mon Jan 24 2005 - 17:04:58 CST

Thank you. Here is Ilya Balabin's reply:


Hi Blake,

this is a good question. In fact, this is the question of the water
density in equilibrium - as you say, one can use the actual (observed
in experiments) density, or TIP3 water density, or something else. In
the plugin, I used the density observed in simulations done in the TBG
a few years ago using NAMD2 and the Charmm22 forcefield (TIP3 water),
which translated to 31.05 cubic Angstroms per molecule. This density
led to the coefficient of 0.0187, which differs by 2% from the number
you get for the TIP3 water. The 2% accuracy for ionic concentration
appears to me sufficient for virtually all practical purposes - unless
one simulates a system that is extraordinary sensitive to the ionic
concentration... but such a system would be very sensitive to other
details of MD simulations as well.

This is how the number of ions is calculated in the autoionize plugin:

N_ions = N_A * ionConc(Mol/l) * volume(l)
N_A = 6.022e23
volume(l) = volume_per_water_molecule(l) * nWater
volume_per_water_molecule = 31.05A^3 = 3.105e-26l
N_ions = 6.022e23 * 3.105e-26 * ionConc * nWater
       = 0.0187 * ionConc * nWater

Yes I would appreciate posting of this to the VMD-l mailing list.

John thanks for the reference! :)


"Research is what I'm doing when I don't know what I'm doing."

-----Original Message-----
From: [] On Behalf Of
John Stone
Sent: January 21, 2005 6:30 PM
To: Blake Charlebois
Subject: Re: vmd-l: Autoionize / SODIUM

  I'd suggest that you contact Ilya Balabin about this detailed
question, he is the author of the autoionize plugin:

  John Stone

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.
> 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
> 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
> arrived at 0.0187?
> I have a protein with charge -13. Suppose I want to add x Na ions and
> 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
> the initial coordinates do not need to be selected too carefully. Does
> anyone have an opinion on this?
> Thank you,
> Blake Charlebois

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