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Parametrisation of time-averaged distance restraints in MD simulations

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Summary

Time-averaged restraints in molecular dynamics simulations offer a means to account for the averaging that is implicit in NMR spectroscopic data. We present a systematic investigation of the parameters which characterise time-averaged distance restraints. Using previously published data for a small protein, chymotrypsin inhibitor 2, we identify conditions which can lead to undesirable heating or which grossly distort the dynamics of the system.

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Abbreviations

NOE:

nuclear Overhauser effect

MD:

molecular dynamics

CI-2:

chymotrypsin inhibitor 2

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Author notes

  1. Andrew E. Torda

    Present address: Research School of Chemistry, Australian National University, 0200, Canberra, Australia

Authors and Affiliations

  1. Department of Physical Chemistry, ETH Zentrum, CH-8092, Zürich, Switzerland

    Alain P. Nanzer, Wilfred F. van Gunsteren & Andrew E. Torda

Authors
  1. Alain P. Nanzer
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  2. Wilfred F. van Gunsteren
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  3. Andrew E. Torda
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Nanzer, A.P., van Gunsteren, W.F. & Torda, A.E. Parametrisation of time-averaged distance restraints in MD simulations. J Biomol NMR 6, 313–320 (1995). https://doi.org/10.1007/BF00197812

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  • DOI: https://doi.org/10.1007/BF00197812

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