[gmx-users] Re: GB-polarization

[Justin A. Lemkul]

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: muecksch at 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,

-- 
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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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