[gmx-users] Poisson-Boltzmann free energy in gromacs?
francesco.oteri at gmail.com
Sun Jul 17 12:36:46 CEST 2011
you can use APBS (Adaptive Poisson-Boltzman Solver,
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.
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
>>> *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
>>> There is no mention of such a feature in the manual, so I would
>>> suspect the answer is no.
>>> -- ========================================
>>> 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
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