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