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

[Francesco Oteri]

Hi Sanku,
you can use APBS (Adaptive Poisson-Boltzman Solver, 
http://www.poissonboltzmann.org/apbs/ ).
This program computes the PB equation on a single conformation, but you 
can write a script to calculate values over trajectory.
APBS has the advances to be integrated into VMD and pymol, moreover is 
avalaible an MPI parallelized version.


Francesco


Il 17/07/2011 02:47, Mark Abraham ha scritto:
> 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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>>
>