Comparison of protein force fields for molecular dynamics simulations.

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Comparison of protein force fields for molecular dynamics simulations. Abstract Text:

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.

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Comparison of protein force fields for molecular dynamics simulations. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Methods in molecular biology (Clifton, N.J.)

VOLUME: 443

Page Numbers: 63-88

Journal Abbreviation: Methods Mol. Biol.

ISSN: 1064-3745

DAY: 30

MONTH: 04

YEAR: 2008

Comparison of protein force fields for molecular dynamics simulations. Information

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LANGUAGE: eng

NlmUniqueID: 9214969

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AFFILIATION: Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD, USA.

Country: United States

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MEDLINETA: Methods Mol Biol

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