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Molecular Dynamics Simulation: From “Ab Initio” to “Coarse Grained”

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Handbook of Computational Chemistry

Abstract

This chapter provides an overview of different hierarchical levels of molecular dynamics (MD) spanning a wide range of time and length scales – from first-principles approaches via classical atomistic methods to coarse-graining techniques. The theoretical background of the most widely used methods and algorithms is briefly reviewed, and practical instructions are given on the choice of input parameters for an actual computer simulation. In addition, important postprocessing procedures such as data analysis and visualization are discussed.

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Authors and Affiliations

  1. Department of Physics, King’s College London, Strand, WC2R 2LS, London, UK

    Chris Lorenz

  2. Institute for Solid State Theory and Center for Multiscale Theory and Computation, University of Münster, Wilhelm-Klemm-Str. 10, 48149, Münster, Germany

    Nikos L. Doltsinis

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Correspondence to Chris Lorenz .

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Editors and Affiliations

  1. Department of Chemistry and Biochemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi, USA

    Jerzy Leszczynski

  2. Faculty of Chemistry, Nicolaus Copernicus University, Toruń, Poland

    Anna Kaczmarek-Kedziera

  3. Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Tomasz Puzyn

  4. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Manthos G. Papadopoulos

  5. Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece

    Heribert Reis

  6. US Army Engineer Research and Development Center, Vicksburg, Mississippi, USA

    Manoj K. Shukla

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Lorenz, C., Doltsinis, N. (2017). Molecular Dynamics Simulation: From “Ab Initio” to “Coarse Grained”. In: Leszczynski, J., Kaczmarek-Kedziera, A., Puzyn, T., G. Papadopoulos, M., Reis, H., K. Shukla, M. (eds) Handbook of Computational Chemistry. Springer, Cham. https://doi.org/10.1007/978-3-319-27282-5_7

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