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72. See supplementary material at http://dx.doi.org/10.1063/1.4897324 for figures comparing NLBC and MD calculations for the Mobley test set.34 The source code (MATLAB) and surface discretizations for running the nonlinear boundary-condition calculations, data files, parameters, and scripts for preparing and running the MD calculations of titratable residues, as well as source code to generate the figures, are freely and publicly available online at https://bitbucket.org/jbardhan/si-nlbc. [Supplementary Material]
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/content/aip/journal/jcp/141/13/10.1063/1.4897324
2014-10-06
2016-12-06

Abstract

We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B , 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

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