Re: ion placement method vs total energy of the system

From: Anurag Sethi (
Date: Mon Apr 30 2012 - 10:36:59 CDT


Autoionize places the ions by randomly substituting solvent molecules with
ions. This can be used for proteins (except for ions at active sites and
other important regions of the protein when the ion is coordinated to
residues like cysteine in the protein).
cionize places ions iteratively at electrostatic minima computed using
Coulumb's law on a large grid. As a result, cionize should give a lower
overall potential energy. Placing ions in this manner is particularly
important for highly charged systems like nucleic acids.


On Mon, Apr 30, 2012 at 09:25, raghav singh <> wrote:

> Hi All,
> have anyone mentioned difference in energy if you use autoionize and
> cionize on the same system?
> any possible explanation? ANYONE!!
> Thank You
> Raghav

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