Dan and Jason,
Thanks a lot!
Gustavo.
On Oct 18, 2012, at 8:48 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Thu Oct 18 2012 - 17:30:11 PDT
