Software News and Updates

Software news and updates carma: A molecular dynamics analysis program

  1. Nicholas M. Glykos*

Article first published online: 17 AUG 2006

DOI: 10.1002/jcc.20482

Issue

Journal of Computational Chemistry

Journal of Computational Chemistry

Volume 27, Issue 14, pages 1765–1768, 15 November 2006

Additional Information

How to Cite

Glykos, N. M. (2006), Software news and updates carma: A molecular dynamics analysis program. Journal of Computational Chemistry, 27: 1765–1768. doi: 10.1002/jcc.20482

Author Information

  1. Department of Molecular Biology and Genetics, Democritus University of Thrace, Dimitras 19, 68100 Alexandroupoli, Greece

*Department of Molecular Biology and Genetics, Democritus University of Thrace, Dimitras 19, 68100 Alexandroupoli, Greece

Publication History

  1. Issue published online: 29 AUG 2006
  2. Article first published online: 17 AUG 2006
  3. Manuscript Accepted: 11 MAR 2006
  4. Manuscript Revised: 11 DEC 2005
  5. Manuscript Received: 23 AUG 2005

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Keywords:

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

Graphical Abstract

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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

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