On Thu, Oct 18, 2012 at 6:35 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
>
> Thanks a lot, Jason.
>
> 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?
>
I'm not quite sure what you mean by "nothing to do". The spacial
arrangement of the atoms defines *where* the dielectric constants are
either intdiel or extdiel. But the spacial arrangement of the system does
not determine how to define those dielectric constants. intdiel = 1
because (in GB) you are xferring from vacuum to solution and extdiel = 80
because you're transferring to water.
This is how the implicit solvent model discriminates between buried and
solvent-exposed residues in a large biomolecule -- that is, buried residues
are not screened by the high solvent dielectric.
At least this is my understanding -- I expect someone will quickly correct
me if I am mistaken.
All the best,
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 - 16:00:03 PDT
