Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics.
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+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 parametrized 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.
Mathematical Institute, University of Oxford , Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK.
Radek
0000-0001-8470-3763
R
Erban
Brownian dynamics; molecular dynamics; multiscale modelling