Standard Article

Molecular Dynamics

  1. Roman Petrenko1,
  2. Jarosław Meller1,2

Published Online: 15 MAR 2010

DOI: 10.1002/9780470015902.a0003048.pub2

eLS

eLS

How to Cite

Petrenko, R. and Meller, J. 2010. Molecular Dynamics. eLS. .

Author Information

  1. 1

    University of Cincinnati, Cincinnati, USA

  2. 2

    Nicholas Copernicus University, Toruń, Poland

Publication History

  1. Published Online: 15 MAR 2010

Abstract

Molecular dynamics (MD) is a widely used technique for computer simulation of complex systems, modelled at the atomic or some coarse-grained level. In this article, basic concepts pertaining to MD simulations are systematically introduced and related to the underlying models of physical systems. The principles of the atomic force fields, representation of the environment, the time evolution of the system, as well as the derivation of kinetic and thermodynamic properties of interest from MD trajectories are discussed. Applications of MD to biological systems are illustrated by examples of large scale studies on protein structure and dynamics, protein–protein interactions, and drug design. Limitations and several recent extensions of classical MD, including Replica Exchange and Steered MD, are discussed in the context of applications to biological systems as well. Related simulation protocols, including Monte Carlo and free energy methods, are summarized, highlighting complementarity and common principles of these molecular simulation approaches.

Key Concepts

  • Computer simulations can be used to facilitate and complement experimental studies of biomolecular systems.

  • Empirical force fields describe interatomic interactions in the system and enable efficient computation of forces in MD simulations.

  • MD is routinely used to study biological macromolecules and their environment.

  • A physical quantity can be measured using MD simulations by taking an arithmetic average over instantaneous values of that quantity obtained from MD trajectories.

  • Other simulation methods, such as Monte Carlo, enhanced sampling and free energy methods, are often being used in conjunction with MD and its extensions.

  • Slow processes can be studied computing the relative free energies of different states.

  • MD and related methods can be applied to systems comprising millions of atoms, providing unique insights into complex biological systems.

Keywords:

  • molecular simulations;
  • force field;
  • Monte Carlo;
  • protein dynamics;
  • steered molecular dynamics;
  • replica exchange molecular dynamics