A sampling problem in molecular dynamics simulations of macromolecules.

J B Clarage; T Romo; B K Andrews; B M Pettitt; G N Phillips

doi:10.1073/pnas.92.8.3288

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A sampling problem in molecular dynamics simulations of macromolecules.

J B Clarage·T Romo·B K Andrews·B M Pettitt·G N Phillips

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Abstract

Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.

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Computer Simulation Crystallography, X-Ray Models, Molecular Myoglobin Protein Conformation Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S.

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J B Clarage, T Romo, B K Andrews, B M Pettitt, G N Phillips. 1995-04-11. A sampling problem in molecular dynamics simulations of macromolecules.. https://doi.org/10.1073/pnas.92.8.3288

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