[gmx-users] PME and solvation free energy for individual ions

[Eric Smoll]

Oliver,

I am very grateful for the reply and the additional references.  I will
take the suggested Roux, Garcia, and Hünenberger studies into account when
planning new simulations.

Best,
Eric

On Fri, Nov 30, 2018 at 6:53 PM Oliver Beckstein <obeckste at asu.edu> wrote:

> You might also want to look at work from Hummer, Hünenberger, and recently
> Rocklin, Mobley and Hünenberger before you decide that you can neglect the
> influence of PME on solvation free energies.
>
> [0] G. Hummer, L. Pratt, and A. Garc ́ıa. Free energy of ionic hydration.
> The Journal of Physical Chemistry, 100(4):1206–1215, 1996.
> [1] M. A. Kastenholz and P. H. Hünenberger. Computation of
> methodology-independent ionic solvation free energies from molecular
> simulations. ii. the hydration free energy of the sodium cation. The
> Journal of Chemical Physics, 124(22):224501, Jun 2006.
> [2] M. M. Reif and P. H. Hünenberger. Computation of
> methodology-independent single-ion solvation properties from molecular
> simulations. iii. correction terms for the solvation free energies,
> enthalpies, entropies, heat capacities, volumes, compressibilities, and
> expansivities of solvated ions. The Journal of Chemical Physics,
> 134(14):144103, Apr 2011.
> [3] G. J. Rocklin, D. L. Mobley, K. A. Dill, and P. H. Hünenberger.
> Calculating the binding free energies of charged species based on
> explicit-solvent simulations employing lattice-sum methods: an accurate
> correction scheme for electrostatic finite-size effects. J Chem Phys,
> 139(18):184103, Nov 2013.
>
>
> > On Nov 30, 2018, at 2:56 PM, Eric Smoll <ericsmoll at gmail.com> wrote:
> >
> > Justin,
> >
> > That is encouraging!  Thanks for the guidance and the rapid reply.
> >
> > Best,
> > Eric
> >
> > On Fri, Nov 30, 2018 at 12:30 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 11/30/18 1:56 PM, Eric Smoll wrote:
> >>> Hello GROMACS users,
> >>>
> >>> In systems that require accounting for long-range electrostatic
> >>> interactions, is there a reasonable MD strategy for calculating the
> >>> solvation free energy of individual ions (I am not worried about ion
> >>> pairs)?  If I use the BAR method, I will be transitioning between a
> >> system
> >>> with a net charge and a system without a net charge.  I am worried this
> >> may
> >>> cause PME artifacts.
> >>
> >> Benoit Roux's group looked at this some years ago. The errors are
> >> negligible, both with respect to PME background neutralizing charge and
> >> box size.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
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> --
> Oliver Beckstein, DPhil * oliver.beckstein at asu.edu
> https://becksteinlab.physics.asu.edu/
>
> Associate Professor of Physics
> Arizona State University
> Center for Biological Physics and Department of Physics
> Tempe, AZ 85287-1504
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>
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> Department of Physics: https://physics.asu.edu/content/oliver-beckstein
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