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

[Oliver Beckstein]

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
>> 
>> --
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>> 
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
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>> 
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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
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USA
	
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