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. cheers Andre On Fri, Aug 9, 2013 at 4:02 AM, Heymman <francis.de.lasa...@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 > out > 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 > interactions. > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Trying-to-replicate-Aqvist-s-results-solvation-free-energy-tp5010407p5010412.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- _____________ Prof. Dr. André Farias de Moura Department of Chemistry Federal University of São Carlos São Carlos - Brazil phone: +55-16-3351-8090 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
