2010/10/18 Antonija Tomić <Antonija.Tomic.irb.hr>
> According to my experience it seems that when GB is 1, the MM part in
> the script is ignored; since whatever I change (dial =2, 4,...) the
>
I don't think this is right. dielc is ignored, since the dielectric is a
non-uniform dielectric specified by intdiel and extdiel, which in turn
depends on its location. Other parameters are not necessarily ignored
(though I don't know what other parameters are there).
Good luck!
Jason
> result for the calculation in vacuum was always the same ???
>
> Antonija
>
>
> Citiram case <case.biomaps.rutgers.edu>:
>
> > On Fri, Oct 15, 2010, Antonija Tomić wrote:
> >
> >> When I choose to calculate both GB (GB=1) and PB (PB=1) in
> >> mm_pbsa_Binding.in script, MM energies, more precisely ELE term, seems
> >> not to depend on dielectric constant, i.e. I always get the same value
> >> for ELE. On the other hand, when I switch off GB calculations (using
> >> GB 0 in mm_pbsa_Binding.in script) values for ELE are scaled according
> >> to selected dielectric constant.
> >
> > There is still an old option (dielc) that allows a uniform
> > dielectric function
> > to be used in MM calculations that don't have any other solvent model.
> This
> > is not of much use for atomic-level models, but can be useful for
> > coarse-grained potentials, or for trying to reproduce literature results
> that
> > use this model, or for other specialized calculations.
> >
> > When you use a solvent model like PB or GB, they have their own,
> non-uniform
> > dielectric models, which are controlled by intdiel and extdiel. The
> value of
> > dielc is ignored.
> >
> > ....dac
> >
> >
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Oct 18 2010 - 05:00:06 PDT
