ABSTRACT
The process of performing a molecular simulation can be divided into two main tasks: (1) the generation of molecular conformations and (2) the evaluation of the potential energy for each of these conformations. The systems we are interested in simulating will typically consist of a protein, DNA, or other biomolecule of interest (possibly a complex of one or more of these) together with some representation of its environment (the solvent plus salt and other small molecules). By a molecular conformation we mean a particular arrangement of the atoms comprising the system of interest. This arrangement is typically described using Cartesian coordinates for the atoms, but internal coordinates and various reduced or coarse-grained descriptions of the system are also popular. Chapter 3 discusses these latter representations. In this chapter we assume a Cartesian coordinate description, although much of the discussion will carry over to the other representations. In addition, other chapters in this book discuss methods for generating conformations and force fields for evaluating the conformational energies.
