first thing that I notice is that you are using PBC whereas Aqvist employed a spherical boundary model. I also think that PME is not applicable for a spherical boundary, so the reciprocal space contributions may be considered as spurious if you want to reproduce the original results. Maybe you should read Aqvist's paper methodology section and compare carefully the description of the original model and yours.
cheers Andre On Thu, Aug 8, 2013 at 5:37 PM, Francis de Lasalle < francis.de.lasa...@umontreal.ca> wrote: > Hello, > > As we're trying to get familiar with Gromacs, in order to be able to > perform solvation free energy calculations of ions, we're trying to > replicate the results obtained by Aqvist (the author of the article from > which were obtained Lennard-Jones parameters for alkaline and alkaline > earth ions, for the OPLS-AA force field). The solvation free energies we're > computing are all about 50 kJ/mol different from the values reported by > Aqvist. We verified that the Lennard-Jones parameters for our ions and for > the water are identical to that of Aqvist and we're also using SPC water. > We're wondering why we can't reproduce these results and any input would be > greatly appreciated. Here's the article : > > http://pubs.acs.org/doi/pdf/**10.1021/j100384a009<http://pubs.acs.org/doi/pdf/10.1021/j100384a009> > > We're using 200 lambda states with 2000000 steps incremented by 0.002 ps > (4000 ps). Here's our run file for Li+ : > > integrator = sd > nsteps = 2000000 > dt = 0.002 > nstenergy = 1 > nstlog = 1 > nstxout = 0 > nstvout = 0 > cutoff-scheme = group > rlist = 1.0 > dispcorr = EnerPres > vdw-type = cut-off > rvdw = 1.0 > coulombtype = pme > rcoulomb = 1.0 > fourierspacing = 0.12 > constraint-algorithm = SHAKE > continuation = no > shake-tol = 0.00001 > constraints = all-angles > tcoupl = v-rescale > tc-grps = system > tau-t = 0.2 > ref-t = 298 > ref-p = 1 > compressibility = 4.5e-5 > tau-p = 5 > free-energy = yes > couple-moltype = lithium > sc-power = 1 > sc-sigma = 0.3 > sc-alpha = 1.0 > couple-intramol = no > couple-lambda1 = vdwq > couple-lambda0 = none > init-lambda-state = $LAMBDA > fep-lambdas = $LAMBDAS > > The box has been equilibrated for 1 ns at 298 K. The box is a dodecahedron > with 240 water molecules. > > Thanks a lot. > > Francis > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
