Christian Mücksch wrote:
But in order to get the complete solvation free energy these
calculations for the van der Waals and cavity terms have to be done.
So does that mean that the solvation free energy calculated by default
without specifying "sa_algorithm=Ace-approximation" is missing these terms?
I thought that the ACE-type approximation is done by default (due to the
manual) when using GBSA.
I think it all depends on the version you're using. Ace-approximation became
default in version 4.5.2 (I think). In previous versions, "no" was the default,
at least such was the case in my testing of 4.5.1.
-Justin
Kind regards,
Christian
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:mueck...@rhrk.uni-kl.de
> > >
>> 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
========================================
--
========================================
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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