title: A sampling problem in molecular dynamics simulations of macromolecules.
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.
authors.affiliation: Keck Center for Computational Biology, Rice University, Houston, TX 77251-1892, USA.
authors.forename: J B
authors.initials: JB
authors.lastname: Clarage
authors.forename: T
authors.initials: T
authors.lastname: Romo
authors.forename: B K
authors.initials: BK
authors.lastname: Andrews
authors.forename: B M
authors.initials: BM
authors.lastname: Pettitt
authors.forename: G N
authors.initials: GN
authors.lastname: Phillips
mesh_terms: D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009211:Myoglobin / Q000737:chemistry*; D011487:Protein Conformation
chemical_list: D009211:Myoglobin