On Tue, Dec 31, 2024, Kankana Bhattacharjee via AMBER wrote:
>
>I have used polarizable water model "OPC3POL" as a water model for my
>calculation. Now, I would like to know, is there any way to include
>additional polarizable continuum model. I mean PCM model or any other model
>is present ? As we are trying to mimic polarizability of water.
The "POL" part of OPC3POL attempts to describe the electronic polarizability
of water. This is a small, but potentially important, part of water's
interactions with solutes and with other water molecules. Traditional
("fixed-charge") water models include such effects, but in a very averaged
way, since they have fewer adjustable paramters to fit to experimental data.
Polarizable continuum models (of which generalized Born is one example) are
very different. They are attempting to describe the electrostatic effects
of water molecules that *are actually present in the physical system, but
which are not present in the model being simulated.* The language generally
used contrasts "explicit solvation" (where each water molecule contributes two
hydrogen atoms and one oxygen atom to the model), and "implicit solvation"
(where one tries to account for water without actually modeling it.)
The "polarization" in a polarizable continuum model arises primarily from
the orientation of water dipoles in a liquid, and not from electronic
polarizability.
(Apologies if you already knew all this; but your question reflects a point
of confusion for many.)
It *is* possible to add PCM to a system that already has some water
molecules, but the point of the PCM is to represent the effect of the
waters that are not present in the model. In general(!), explicit solvent
models seem to be more accurate than implicit ones, so you may want to
have a reason to consider the latter: ease of setup, enhanced sampling of
conformational space, simplicity for docking calcualations, and so on.
...hope this helps...best wishes for the New Year!....dac
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Received on Wed Jan 01 2025 - 10:30:01 PST
