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Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality.

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.

SUBMITTER: Koller AN

PROVIDER: S-EPMC2426661 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature

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Starting structure dependence of NMR order parameters derived from MD simulations: implications for judging force-field quality.

Koller Alrun N AN Schwalbe Harald H Gohlke Holger H

Biophysical journal 20080425 1

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 ...[more]

PMID: 18441027

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