Literature DB >> 28152306

Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies.

Thomas Simonson1, Gerhard Hummer2,3, Benoît Roux4,5.   

Abstract

Condensed-phase simulations commonly use periodic boundary conditions (PBCs) to represent the thermodynamic limit. For the vapor to liquid transfer of an ion, the gas/liquid boundary and its associated potential change are then missing. Furthermore, the electric potential and field at a given point are given by conditionally convergent infinite series, for which different summation schemes give different results. Nevertheless, standard simulation protocols can be used to compute experimental quantities unambiguously. In particular, using an auxiliary test particle and a multistep solvation path, we show that particle-based, Ewald, and common molecule-based summation schemes for the potential and field are all essentially equivalent. However, all methods require prior knowledge of the gas/liquid boundary potential to compute ionic solvation free energies using PBC protocols for both force-field and quantum-mechanical models.

Entities:  

Year:  2017        PMID: 28152306     DOI: 10.1021/acs.jpca.6b12691

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  4 in total

1.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

2.  Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.

Authors:  Nicolas Panel; Francesco Villa; Ernesto J Fuentes; Thomas Simonson
Journal:  Biophys J       Date:  2018-03-13       Impact factor: 4.033

3.  A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Theory Comput       Date:  2018-02-07       Impact factor: 6.006

4.  Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins.

Authors:  Olivier Bignucolo; Christophe Chipot; Stephan Kellenberger; Benoît Roux
Journal:  J Phys Chem B       Date:  2022-09-01       Impact factor: 3.466

  4 in total

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