Comparison of protein force fields for molecular dynamics simulations.

Printer-friendly versionPrinter-friendly versionPDF versionPDF version
TitleComparison of protein force fields for molecular dynamics simulations.
Publication TypeJournal Article
Year of Publication2008
AuthorsGuvench, O, Mackerell, AD
JournalMethods Mol Biol
Volume443
Pagination63-88
Date Published2008
ISSN1064-3745
KeywordsCarbohydrates, Computer Simulation, Lipids, Nucleic Acids, Protein Conformation, Protein Folding, Proteins, Software, Temperature
Abstract

In the context of molecular dynamics simulations of proteins, the term "force field" refers to the combination of a mathematical formula and associated parameters that are used to describe the energy of the protein as a function of its atomic coordinates. In this review, we describe the functional forms and parameterization protocols of the widely used biomolecular force fields Amber, CHARMM, GROMOS, and OPLS-AA. We also summarize the ability of various readily available noncommercial molecular dynamics packages to perform simulations using these force fields, as well as to use modern methods for the generation of constant-temperature, constant-pressure ensembles and to treat long-range interactions. Finally, we finish with a discussion of the ability of these force fields to support the modeling of proteins in conjunction with nucleic acids, lipids, carbohydrates, and/or small molecules.

DOI10.1007/978-1-59745-177-2_4
Alternate JournalMethods Mol. Biol.
PubMed ID18446282
Grant ListF32CA119771 / CA / NCI NIH HHS / United States
R01GM051501 / GM / NIGMS NIH HHS / United States
R01GM070855 / GM / NIGMS NIH HHS / United States