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Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations

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Computational Molecular Dynamics: Challenges, Methods, Ideas

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

Abstract

A personal account of work on long-timestep integration of biomolecular dynamics is presented, emphasizing the limitations, as well as success, of various approaches. These approaches include implicit discretization, separation into harmonic and anharmonic motion, and force splitting; some of these techniques are combined with stochastic dynamics. A Langevin/force-splitting approach for biomolecular simulations termed LN (for its origin in a Langevin/normal-modes scheme) is also described, suitable for general thermodynamic and sampling questions. LN combines force linearization, stochastic dynamics, and force splitting via extrapolation so that the timestep for updating the slow forces can be increased beyond half the period of the fast motions (i.e., 5 fs). This combination of strategies alleviates the severe stability restriction due to resonance artifacts that apply to symplectic force-splitting methods and can yield significant speedup (with respect to small-timestep reference Langevin trajectories). Extensions to sampling problems are natural by this approach.

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Authors and Affiliations

  1. Department of Chemistry and Courant Institute of Mathematical Sciences, New York University and The Howard Hughes Medical Institute, 251 Mercer Street, New York, NY, 10012, USA

    Tamar Schlick

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  1. Tamar Schlick
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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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Schlick, T. (1999). Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations. 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_13

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