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Computational Molecular Dynamics: Challenges, Methods, Ideas pp 39–65Cite as

Steered Molecular Dynamics

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Part of the book series: Lecture Notes in Computational Science and Engineering ((LNCSE,volume 4))

Abstract

Steered molecular dynamics (SMD) induces unbinding of ligands and conformational changes in biomolecules on time scales accessible to molecular dynamics simulations. Time-dependent external forces are applied to a system, and the responses of the system are analyzed. SMD has already provided important qualitative insights into biologically relevant problems, as demonstrated here for applications ranging from identification of ligand binding pathways to explanation of elastic properties of proteins. First attempts to deduce potentials of mean force by discounting irreversible work performed on the system are summarized. The non-equilibrium statistical mechanics underlying analysis of SMD data is outlined.

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Authors and Affiliations

  1. Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews, Urbana, IL, 61801, USA

    Sergei Izrailev, Sergey Stepaniants, Barry Isralewitz, Dorina Kosztin, Hui Lu, Ferenc Molnar, Willy Wriggers & Klaus Schulten

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  1. Sergei Izrailev
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  2. Sergey Stepaniants
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  3. Barry Isralewitz
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  4. Dorina Kosztin
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  5. Hui Lu
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  6. Ferenc Molnar
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Editors and Affiliations

  1. Konrad-Zuse-Zentrum Berlin (ZIB), Takustrasse 7, D-14195, Berlin-Dahlem, Germany

    Peter Deuflhard

  2. Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27599-7260, USA

    Jan Hermans

  3. Department of Mathematics, University of Kansas, 405 Snow Hall, Lawrence, KS, 66045, USA

    Benedict Leimkuhler

  4. Laboratorium für Physikalische Chemie ETH Zentrum, CH-8092, Zürich, Switzerland

    Alan E. Mark

  5. Department of Mathematics and Statistics, University of Surrey, Guildford, Surrey, GU2 5XH, UK

    Sebastian Reich

  6. Department of Computer Science, University of Illinois, 1304 West Springfield Avenue, Urbana, IL, 61801-6631, USA

    Robert D. Skeel

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Izrailev, S. et al. (1999). Steered Molecular Dynamics. In: Deuflhard, P., Hermans, J., Leimkuhler, B., Mark, A.E., Reich, S., Skeel, R.D. (eds) Computational Molecular Dynamics: Challenges, Methods, Ideas. Lecture Notes in Computational Science and Engineering, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-58360-5_2

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  • DOI: https://doi.org/10.1007/978-3-642-58360-5_2

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