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Classical Molecular Dynamics in a Nutshell

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Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 924))

Abstract

This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton’s equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms and molecules with each other. It also illustrates algorithms used to simulate systems at constant temperature and/or pressure and discusses their advantages and disadvantages. It presents a few methods to save CPU time and a summary of popular software for biomolecular molecular dynamics simulations.

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Acknowledgments

I would like to thank Markus Miettinen for providing some of the figures and Mikko Karttunen for reading the manuscript.

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Authors and Affiliations

  1. Department of Applied Mathematics, University of Western Ontario, London, ON, Canada

    Susanna Hug

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  1. Susanna Hug
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Editors and Affiliations

  1. DSIMB, UMR-S 665, INSERM, rue Alexandre Cabanel 6, Paris, 75015, France

    Luca Monticelli

  2. , Department of Applied Physics, Aalto University, Otakaari, AALTO, FI-00076, Finland

    Emppu Salonen

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Hug, S. (2013). Classical Molecular Dynamics in a Nutshell. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_6

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  • DOI: https://doi.org/10.1007/978-1-62703-017-5_6

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  • Publisher Name: Humana Press, Totowa, NJ

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