[gmx-users] Re: GB-polarization

[Per Larsson]

Hi!

Sorry for the confusion here. Justin is right. In versions before 4.5.2, the non-polar solvation calculation was done regardless of the sa_algorithm setting.
In 4.5.2, this has to be specified explicitly using the setting Ace-approximation, to get the complete solvation free energy.

Also, the value of sa_surface_tension was set automatically in versions up to 4.5.1. In 4.5.2, this is also the case as long as it is set to -1 in the mdp-file. Setting it to 0 means no non-polar calculation is done, and setting it to something else (but non-zero) will override the default values (eg. those that were always used in 4.5.1)

Again, sorry for the confusion. 

I will update the manual to make this more clear.

/Per


Skickat från min iPhone

9 nov 2010 kl. 23:53 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:

> 
> 
> 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
> 
> ========================================
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists