title: Molecular dynamics simulations: bring biomolecular structures alive on a computer.
abstract: The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.
authors.affiliation: Centre for Computational Science, Chemistry Department, University College of London, UK.
authors.forename: Shunzhou
authors.initials: S
authors.lastname: Wan
authors.forename: Peter V
authors.initials: PV
authors.lastname: Coveney
authors.forename: Darren R
authors.initials: DR
authors.lastname: Flower
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D015789:HLA-A2 Antigen / Q000737:chemistry; D006801:Humans; D007125:Immunogenetics; D008285:Major Histocompatibility Complex; D008958:Models, Molecular; D046912:Multiprotein Complexes; D010455:Peptides / Q000737:chemistry / Q000276:immunology; D012984:Software; D013816:Thermodynamics
chemical_list: D015789:HLA-A2 Antigen; D046912:Multiprotein Complexes; D010455:Peptides