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Keywords:

  • molecular dynamics;
  • principal component analysis;
  • essential dynamics;
  • trajectory viewer

Abstract

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006