[gmx-users] Trying to replicate Aqvist's results (solvation free energy).

[André Farias de Moura]

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.lasalle at 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
>
>
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090