title: Classical molecular dynamics in a nutshell.
abstract: This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton's equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms and molecules with each other. It also illustrates algorithms used to simulate systems at constant temperature and/or pressure and discusses their advantages and disadvantages. It presents a few methods to save CPU time and a summary of popular software for biomolecular molecular dynamics simulations.
authors.affiliation: Department of Applied Mathematics, University of Western Ontario, London, ON, Canada.
authors.forename: Susanna
authors.initials: S
authors.lastname: Hug
mesh_terms: D000465:Algorithms; D001704:Biopolymers / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D011312:Pressure; D012984:Software; D013696:Temperature
chemical_list: D001704:Biopolymers