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

Discussion:

Eric Smoll

2018-11-30 18:56:33 UTC

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.

Best,
Eric

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Justin Lemkul

2018-11-30 19:30:02 UTC

Permalink

Post by Eric Smoll
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.

Eric Smoll

2018-11-30 19:56:41 UTC

Permalink

Justin,

That is encouraging! Thanks for the guidance and the rapid reply.

Best,
Eric

Post by Eric Smoll

system

Post by Eric Smoll
with a net charge and a system without a net charge. I am worried this

may

Post by Eric Smoll
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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Office: 301 Fralin Hall
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Oliver Beckstein

2018-12-01 01:53:24 UTC

Permalink

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.

Post by Eric Smoll
Justin,
That is encouraging! Thanks for the guidance and the rapid reply.
Best,
Eric

Post by Eric Smoll

system

Post by Eric Smoll
with a net charge and a system without a net charge. I am worried this

may

Post by Eric Smoll
cause PME artifacts.

--
Oliver Beckstein, DPhil * ***@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
USA

Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669

Department of Physics: https://physics.asu.edu/content/oliver-beckstein
Center for Biological Physics: https://cbp.asu.edu/content/oliver-beckstein

Eric Smoll

2018-12-01 02:34:58 UTC

Permalink

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

Post by 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.

Post by Eric Smoll
Justin,
That is encouraging! Thanks for the guidance and the rapid reply.
Best,
Eric

Post by Eric Smoll

system

Post by Eric Smoll
with a net charge and a system without a net charge. I am worried this

may

Post by Eric Smoll
cause PME artifacts.

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Gromacs Users mailing list
* Please search the archive at

http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!

Post by Eric Smoll
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--
https://becksteinlab.physics.asu.edu/
Associate Professor of Physics
Arizona State University
Center for Biological Physics and Department of Physics
Tempe, AZ 85287-1504
USA
Office: PSF 348
Phone: +1 (480) 727-9765
FAX: +1 (480) 965-4669
Department of Physics: https://physics.asu.edu/content/oliver-beckstein
https://cbp.asu.edu/content/oliver-beckstein
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