Application of molecular dynamics simulation in self-assembly

Abstract

During the past few years, numerous studies have been done in self-assembly. Among most of these studies, Molecular Dynamic Simulation is widely used to construct the experiment model. This work firstly introduced three practical applications of MD simulation in self-assembly. Then, two main kinds of simulation are discussed including all-atom simulation and coarse-grained simulation, together with the way of thoughts before the simulation start. It is found that researchers always start with the whole analysis of the substances that need to be studied. It helps to confirm the appropriate model that can apply in the simulation naturally. Besides, depended on the principles that need to be studied, the way of establishing the simulation system varies, ranging from separation experiment in both types of simulation to the change of essential parameters. Furthermore, the adoption of L-J potential in MD simulation proves to be a wise option on account of its convenient and simple model. It is remarkable that, considering some small details like the differences between implicit and explicit solution, classical Martini force field is replaced by Dry Martini force field.