A sampling problem in molecular dynamics simulations of macromolecules

James B. Clarage, Tod Romo, B. Kim Andrews, B. Montgomery Pettitt, George N. Phillips

Research output: Contribution to journalArticle

152 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)3288-3292
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Volume92
Issue number8
DOIs
StatePublished - Apr 11 1995

Keywords

  • crystallography
  • dynamical systems
  • phase space
  • protein flexibility
  • x-ray diffuse scattering

ASJC Scopus subject areas

  • General

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