Re: [AMBER] intdiel / extdiel

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 18 Oct 2012 15:26:22 -0400

On Thu, Oct 18, 2012 at 2:01 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:

> Hi folks,
>
> I have yet another question regarding the definition of "intdiel". I
> understand it is supposedly the dialectric constant "inside" the molecule,
> as have been discussed previously:
>
> http://archive.ambermd.org/201007/0705.html
> http://archive.ambermd.org/200211/0148.html
>
> However, the manual says it a bit differently:
> "[] the interior of the atom is assumed to be filled uniformly with a
> material of dielectric constant 1." (page 47),
>
> Then when describing intdiel:
> "intdiel Sets the interior dielectric constant of the molecule of
> interest. Default is 1.0. Other values have not been extensively tested."
> (page 52).
>
> My question is about what exactly is set by intdiel. Is it the dielectric
> in the interior of the ATOM (as within the limits of the atomic radius) or
> is it the constant in the interior of the MOLECULE (for example, as within
> a certain radius from the COM of the molecule)?
>

In GB (like in PB), the environment is roughly partitioned into two
dielectric regions, the interior of the molecule (solvent inaccessible, low
internal dielectric) and the exterior of the molecule (solvent accessible,
high external dielectric).

In GB, the 'effective radius' is basically an average measure of how far
away a given atom is from the solvent-accessible region (following the Born
solution of the PB equation to solvating a single charged particle). The
picture in GB is a little different compared to PB, though.

In PB, the interior dielectric really is the dielectric constant of the
interior of the protein (sometimes set to ~2 to account for electron
polarization). In GB, the 'internal' dielectric constant is actually the
dielectric constant of the medium you're transferring *from*. That is, GB
measures the free energy of transferring a structure from gas
(dielectric=1) to solution (dielectric=80), so intdiel actually means
something different in GB compared to PB. (In the derivation of the GB
equation, the internal dielectric of the solute actually cancels out)

What people have done is to set the interior dielectric to != 1 in GB and
said that was equivalent to transferring the solute from a low-dielectric,
organic solvent with the same dielectric response as the interior of the
solute, into the high-dielectric, polar solvent.

Hopefully this is clear-ish,
Jason

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 18 2012 - 12:30:02 PDT
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