[gmx-users] Re: Trying to replicate Aqvist's results (solvation free energy).
André Farias de Moura
moura at ufscar.br
Fri Aug 9 15:00:30 CEST 2013
never done that calculation myself, so it's hard to say if these
differences in the setup may account for such a free energy difference, but
I remember one lecture by Phillipe Hünenberger a few years ago when he
presented a large compilation of hydration free energies for sodium and the
figures changed quite a lot from one simulation to the next, so I wouldn't
be surprised if your setup produces a result differing from Aqvist's
original report by 50 kJ/mol.
I don't think that GROMACS allows you to reproduce the exact setup that was
used by Aqvist back then, so if you want to get familiar with the free
energy calculations as implemented in GROMACS maybe you should try to
reproduce some other more recent calculation using this software, because
this is the only way we have guarantees that model systems match each other
and that results should match too.
On Fri, Aug 9, 2013 at 4:02 AM, Heymman <francis.de.lasalle at umontreal.ca>wrote:
> Thank you for posting. I also noticed they were using a spherical boundary
> model; you think using PBC would justify a 50 kJ/mol difference ? As for
> PME, we wanted to use the classical Ewald summation method, but it turns
> that Gromacs hasn't implemented it, yet, for free energy of solvation
> calculations. Other than that, the only noticeable difference I could find
> concerns the choice of cutoff radius for ion-water and water-water
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Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
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