From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Jul 18 2013 - 21:09:27 CDT
On Thu, Jul 18, 2013 at 9:02 PM, adrian palacios <adpala_at_hotmail.com> wrote:
> But doing so, using this implicit model, I could be able to track the
> position or radial distribution of ions?
>
No. The only implicit solvent model that can reliably predict RDFs that
I'm aware of is 3D-RISM (and related) methods. In general, explicit
solvent models (with carefully derived ion parameters) are the only way for
you to obtain this data.
Even if you added explicit ions to implicit solvent simulations, the fact
that your system is infinitely dilute means you cannot track ion positions
or ion RDFs in a meaningful way.
> or I could be able to obtain the electric potential at a certain distances
> from the molecule considering the specific/local screening?
>
The screening is incorporated in a mean field way (I believe it
approximates the linearized PB equation). The standard GB equation
derives from the solvation free energy from the solution of the Poisson
equation for a charged sphere in solution (the Born equation). While you
may be able to back out the original electrostatic potential from the
computed free energies, I would argue that the PB equation is far better
suited for this kind of analysis (although GB has many advantages over PB
in dynamics).
It sounds to me like you are better off sticking to explicit solvent
simulations.
Good luck,
Jason
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