Parametrisation of time-averaged distance restraints in MD simulations |
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| Authors: | Alain P Nanzer Wilfred F van Gunsteren Andrew E Torda |
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| Institution: | (1) Department of Physical Chemistry, ETH Zentrum, CH-8092 Zürich, Switzerland;(2) Present address: Research School of Chemistry, Australian National University, 0200 Canberra, Australia |
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| Abstract: | 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.Abbreviations NOE
nuclear Overhauser effect
- MD
molecular dynamics
- CI-2
chymotrypsin inhibitor 2 |
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| Keywords: | Time-averaged distance restraints Parametrisation MD simulation |
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