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

Radek Erban

doi:10.1098/rspa.2015.0556

Abstract

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.

Highlights

Molecular dynamics (MD) simulations of ions in aqueous solutions are limited to modelling processes in relatively small domains containing several thousands of water molecules [1,2]
Our goal is to show that the coarse-grained model (1.2)–(1.5) is an intermediate model between all-atom MD and Brownian dynamics (BD) which enables the use of both methods during the same dynamic simulation
We have introduced and studied the coarse-grained model (1.2)–(1.5) of an ion in aqueous solution

Summary

Introduction

Molecular dynamics (MD) simulations of ions in aqueous solutions are limited to modelling processes in relatively small domains containing (only) several thousands of water molecules [1,2]. The calcium-induced calcium release through IP3R channels is an example of a multiscale dynamical problem where MD simulations are important only in certain parts of the computational domain (close to an IP3R channel), while in the remainder of the domain a coarser, less detailed, BD method could be used (to describe trajectories of ions). Considering all-atom MD simulations, the coarser stochastic model of an ion is more complicated than Langevin dynamics In this paper, it will be given by dXi = Vi dt,. We express mass in daltons (Da), length in ångströms (Å) and time in picoseconds (ps), consistently in the whole paper Using these units, the parameters of the Lennard–Jones potential between the oxygen sites on two SPC/E water molecules are Aoo = 2.6334 × 108 Da Å14 ps−2 and Boo = 2.6171 × 105 Da Å8 ps−2.

Parametrization of the coarse-grained model of ion

Accuracy of the coarse-grained model of ion

From the coarse-grained model to Brownian dynamics

Coupling all-atom MD and BD

A hierarchy of stochastic coarse-grained models

Discussion