Basics of Molecular Dynamics Simulation Methods

This chapter provides an overview of molecular dynamics (MD) simulation method used in the molecular modeling and simulation of composite and fiber/matrix interfaces. The objective is to introduce the fundamental basics, including definition, theory, and techniques used in MD simulation. The knowledge related to molecular mechanics including the molecular modeling, forcefield, boundary conditions, and energy minimization method is firstly presented. Afterwards, MD simulation procedures are summarized, which consist of ensemble assignment, integration algorithm selection, relaxation and simulation, data analysis and post-processing, as well as trajectory analysis.