Molecular dynamics simulation: From “ab initio” to “coarse grained”

Abstract

This chapter provides an overview of different hierarchical levels of molecular dynamics (MD) simulations spanning a wide range of time and length scales - from first principles approaches via classical atomistic methods to coarse graining techniques.The theoretical background of the most widely used methods and algorithms is briefly reviewed and practical instructions are given on the choice of input parameters for an actual computer simulation. In addition, important postprocessing procedures such as data analysis and visualization are discussed.