[gmx-users] Poisson-Boltzmann free energy in gromacs?

[Mark Abraham]

On 17/07/2011 10:45 AM, Justin A. Lemkul wrote:
>
>
> Sanku M wrote:
>> I thought since the implicit solvent model has been invoked recently, 
>> there might be some features for PB calculation as well.
>>
>
> You can get GB polarization energies with the implicit solvent code, 
> but not PB, as far as I am aware.  If there are undocumented features, 
> perhaps one of the developers can comment.  But given the lack of any 
> documentation on the matter, I would conclude that direct PB 
> calculations cannot be done at present.

They can't

Mark

>
> -Justin
>
>> ------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* Discussion list for GROMACS users <gmx-users at gromacs.org>
>> *Sent:* Sat, July 16, 2011 7:35:43 PM
>> *Subject:* Re: [gmx-users] Poisson-Boltzmann free energy in gromacs?
>>
>>
>>
>> Sanku M wrote:
>> > Hi,
>> >  I was wondering whether, in gromacs,  there is any way of 
>> calculating the electrostatic free energy using poisson Boltzmann 
>> equation.
>>
>> There is no mention of such a feature in the manual, so I would 
>> suspect the answer is no.
>>
>> -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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>