An iterative, fast, linear-scaling method for computing induced charges on arbitrary dielectric boundaries.
Simulating coarse-grained models of charged soft-condensed matter systems in presence of dielectric discontinuities between different media requires an efficient calculation of polarization effects. This is almost always the case if implicit solvent models are used near interfaces or large macromolecules. We present a fast and accurate method (ICC( small star, filled)) that allows to simulate the presence of an arbitrary number of interfaces of arbitrary shape, each characterized by a different dielectric permittivity in one-, two-, and three-dimensional periodic boundary conditions. The scaling behavior and accuracy of the underlying electrostatic algorithms allow to choose the most appropriate scheme for the system under investigation in terms of precision and computational speed. Due to these characteristics the method is particularly suited to include nonplanar dielectric boundaries in coarse-grained molecular dynamics simulations.
Tyagi
Sandeep
S
Frankfurt Institute for Advanced Studies (FIAS), Ruth-Moufang-Str. 1, 60438 Frankfurt am Main, Germany.
Süzen
Mehmet
M
Sega
Marcello
M
Barbosa
Marcia
M
Kantorovich
Sofia S
SS
Holm
Christian
C
D000465:Algorithms; D056004:Molecular Dynamics Simulation; D055672:Static Electricity