Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

doi:10.1073/pnas.0408037102

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

Department of Chemistry, Yale University, New Haven, CT 06520-8107

Edited by Bruce J. Berne, Columbia University, New York, NY, and approved March 14, 2005 (received for review November 17, 2004)

Abstract

An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.

Footnotes

↵ * To whom correspondence should be addressed. E-mail: william.jorgensen{at}yale.edu.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: AA, all-atom; MC, Monte Carlo; MD, molecular dynamics; MCY, Matsuoka Clementi Yoshimine; MM, molecular mechanics; OPLS, optimized potentials for liquid simulations; PI, path integral; QM, quantum mechanics; QM/MM, quantum and molecular mechanics; rdf, radial distribution function; TMD, temperature of maximum density.