Christian Mücksch wrote:
Thanks for the clarification but I can't find anything in the .log or
.edr-files that would correspond to the non-polar solvation energy.
I think you have to set "sa_algorithm=Ace-approximation" for this calculation to
be done, and thus written.
-Justin
Christian Mücksch
Department of Physics
TU Kaiserslautern
Erwin Schrödinger Straße
67663 Kaiserslautern
Germany
Phone: +49 (0)631 205 4287
Fax: +49 (0)631 205 4965
Email: [email protected]
Hi! Yes, the GB-polarization energy corresponds to the solvent-solute
electrostatics polarization energy. The non-polar part of the
solvation energy (the solvent-solvent cavity term and the
solute-solvent vdw-term) are named Non. polar solvation (or something
like that) in the log-file. /Per 4 nov 2010 kl. 11.10 skrev Christian
Mücksch:
> Dear all,
> > I've got a general question regarding implicit solvent
simulations.
> Using g_energy there's an option to print out the GB-polarization.
Is that the solvent-solute electrostatics polarization free energy?
> > How can one interpret a rise or decrease in the GB-polarization?
> > Kind regards,
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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