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Atomistic Force Fields for Proteins

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Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2022))

Abstract

All-atom, classical force fields for protein molecular dynamics (MD) simulations currently occupy a sweet spot in the universe of computational models, sufficiently detailed to be of predictive value in many cases, yet also simple enough that some biologically relevant time scales (microseconds or more) can now be sampled via specialized hardware or enhanced sampling methods. However, due to their long evolutionary history, there is now a myriad of force field branches in current use, which can make it hard for those entering the simulation field to know which would be the best set of parameters for a given application. In this chapter, I try to give an overview of the historical motivation for the different force fields available, suggestions for how to determine the most appropriate model and what to do if the results are in conflict with experimental evidence.

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Acknowledgment

RB is supported by the Intramural Research Program of the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health.

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Authors and Affiliations

  1. Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA

    Robert B. Best

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  1. Robert B. Best
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Correspondence to Robert B. Best .

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Editors and Affiliations

  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Best, R.B. (2019). Atomistic Force Fields for Proteins. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9608-7_1

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