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Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics (1508.02805v1)
Published 12 Aug 2015 in physics.comp-ph and q-bio.SC
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.