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Time-averaged order parameter restraints in molecular dynamics simulations

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Abstract

A method is described that allows experimental \(S^2\) order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N–H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.

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Acknowledgments

This work was financially supported by the National Center of Competence in Research (NCCR) in Structural Biology and by Grant Number 200020-137827 of the Swiss National Science Foundation, and by grant number 228076 of the European Research Council, which is gratefully acknowledged. N.H. thanks the German Research Foundation (DFG) for financial support within the Cluster of Excellence in Simulation Technology (EXC 310/1) at the University of Stuttgart.

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  1. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland

    Niels Hansen, Fabian Heller, Nathan Schmid & Wilfred F. van Gunsteren

  2. Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, 70569, Stuttgart, Germany

    Niels Hansen

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  1. Niels Hansen
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Hansen, N., Heller, F., Schmid, N. et al. Time-averaged order parameter restraints in molecular dynamics simulations. J Biomol NMR 60, 169–187 (2014). https://doi.org/10.1007/s10858-014-9866-7

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