[gmx-users] Re: GB-polarization

[Justin A. Lemkul]

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: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 
> ========================================
> 
> 

-- 
========================================

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

========================================