[gmx-users] Re: GB-polarization

[Christian Mücksch]

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.

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: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,
-- ======================================== 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 
========================================