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Communication: Modeling charge-sign asymmetric solvation free energies with
nonlinear boundary conditions
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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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We show that charge-sign-dependent asymmetric hydration can be modeled accurately using
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 112, 2405–2414
(2008)]. Remarkably, the model also justifies the use of linear response expressions for
energies. Our boundary-element method implementation demonstrates the
ease with which other continuum-electrostatic solvers can be extended to include
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