Hi,
On Thu, Oct 18, 2012 at 4:35 PM, Gustavo Seabra
<gustavo.seabra.gmail.com> wrote:
> So, from what I gather, the intdiel/extdiel constants in fact have *nothing to do* with the spacial arrangement of the atoms (except from the calculation of the solvent-accessible area), but just define the free energy term of bringing the whole molecule from one medium to another, is that correct?
For GB, this is correct; the dielectric terms are actually part of a
factor which has nothing to do with the spatial arrangement of the
atoms:
EGB ~ (1/e0 - 1/e) * .5 * SUM[ qiqj / fGB(rij) ]
For PB, the dielectric boundary does depend on the spatial arrangement
of the atoms.
-Dan
>
> Gustavo.
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University of Utah
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Received on Thu Oct 18 2012 - 17:00:03 PDT
