A SAMPLING PROBLEM IN MOLECULAR-DYNAMICS SIMULATIONS OF MACROMOLECULES

Correlations in low-frequency atomic displacements predicted by molecu lar 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 macromolecul e: the reciprocal space of crystallography using diffuse x-ray scatter ing data, real three-dimensional Cartesian space using covariance matr ices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visua lize the extent to which phase space is sampled.