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arXiv · 1508.02805

Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

Radek Erban
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Abstract

Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

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Radek Erban. 2015-08-12. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics. https://doi.org/10.1098/rspa.2015.0556

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