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Updated: Jul 5, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
Published on: December 16, 2013
Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging
Alrun N Koller1, Harald Schwalbe, Holger Gohlke
1Department of Biological Sciences, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Goethe-University, Frankfurt am Main, Germany.
Abstract:
Comparing experimental generalized N-H S(2) order parameters to those calculated from molecular dynamics trajectories is increasingly used to judge force-field quality and completeness of sampling. Herein we demonstrate for the well-investigated system hen egg white lysozyme that different experimental starting structures can lead to significant differences in molecular-dynamics-derived S(2) parameters that can be even larger than S(2) parameter deviations due to different force fields. Caution should thus be taken in general when simulated S(2) parameters are compared to experimental data with the aim of judging force-field quality. We show that adequately sampling flexible regions ( approximately 100 ns) and only calculating S(2) parameters averaged over short time windows proved necessary to obtain consistent results irrespective of the starting structure.
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