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Molecular Dynamics Simulation of Proteins

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Protein Nanotechnology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2073))

Abstract

Molecular dynamics simulations allow the conformational motion of a molecule such as a protein to be followed over time at atomic-level detail. Several choices need to be made prior to running a simulation, including the software, which molecules to include in the simulation, and the force field used to describe their behavior. Guidance on making these choices and other important aspects of running MD simulations is outlined here.

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Acknowledgments

This work was supported financially by DSTL (T.J.P.) and a Rutherford Discovery Fellowship (15-MAU-001) and Marsden grant (15-UOA-105) (J.R.A.).

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Authors and Affiliations

  1. Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand

    Thomas A. Collier & Jane R. Allison

  2. Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand

    Thomas A. Collier & Jane R. Allison

  3. Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory, Wiltshire, UK

    Thomas J. Piggot

  4. School of Chemistry, University of Southampton, Southampton, UK

    Thomas J. Piggot

  5. Biomolecular Interaction Centre, University of Canterbury, Auckland, New Zealand

    Jane R. Allison

  6. School of Biological Sciences, University of Auckland, Auckland, New Zealand

    Jane R. Allison

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  1. Thomas A. Collier
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  2. Thomas J. Piggot
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  3. Jane R. Allison
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Correspondence to Jane R. Allison .

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Editors and Affiliations

  1. School of Biological Sciences, The MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical Sciences, University of Auckland, Auckland, New Zealand

    Juliet A. Gerrard

  2. School of Biological Sciences, Department of Chemical and Materials Engineering, The MacDiarmid Institute for Advanced Materials and Nanotechnology, University of Auckland, Auckland, New Zealand

    Laura J. Domigan

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Collier, T.A., Piggot, T.J., Allison, J.R. (2020). Molecular Dynamics Simulation of Proteins. In: Gerrard, J., Domigan, L. (eds) Protein Nanotechnology. Methods in Molecular Biology, vol 2073. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9869-2_17

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  • DOI: https://doi.org/10.1007/978-1-4939-9869-2_17

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