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Computational Methods for Macromolecules: Challenges and Applications pp 73–103Cite as

A Test Set for Molecular Dynamics Algorithms

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Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 24))

Abstract

This article describes a collection of model problems for aiding numerical analysts, code developers and others in the design of computational methods for molecular dynamics (MD) simulation. Common types of calculations and desirable features of algorithms are surveyed, and these are used to guide selection of representative models. By including essential features of certain classes of molecular systems, but otherwise limiting the physical and quantitative details, it is hoped that the test set can help to facilitate cross-disciplinary algorithm and code development efforts.

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, Kalamazoo College, Kalamazoo, MI, 49006, USA

    Eric Barth

  2. Department of Mathematics and Computer Science, University of Leicester, Leicester, LE1 7RH, UK

    Benedict Leimkuhler

  3. Department of Mathematics, Imperial College, London, SW7 2BZ, UK

    Sebastian Reich

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  1. Eric Barth
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  2. Benedict Leimkuhler
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  3. Sebastian Reich
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  1. Department of Chemistry, Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

  2. Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick  & Hin Hark Gan  & 

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Barth, E., Leimkuhler, B., Reich, S. (2002). A Test Set for Molecular Dynamics Algorithms. In: Schlick, T., Gan, H.H. (eds) Computational Methods for Macromolecules: Challenges and Applications. Lecture Notes in Computational Science and Engineering, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-56080-4_4

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