Software News and Updates
Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories
Article first published online: 15 JUL 2013
Copyright © 2013 Wiley Periodicals, Inc.
Journal of Computational Chemistry
Volume 34, Issue 26, pages 2310–2312, 5 October 2013
How to Cite
How to cite this article: J. Comput. Chem. 2013, 34, 2310–2312. DOI: 10.1002/jcc.23381, .
- Issue published online: 5 SEP 2013
- Article first published online: 15 JUL 2013
- Manuscript Accepted: 25 JUN 2013
- Manuscript Received: 25 APR 2013
- molecular dynamics • principal component analysis • graphical user interface
We report the availability of grcarma, a program encoding for a fully automated set of tasks aiming to simplify the analysis of molecular dynamics trajectories of biological macromolecules. It is a cross-platform, Perl/Tk-based front-end to the program carma and is designed to facilitate the needs of the novice as well as those of the expert user, while at the same time maintaining a user-friendly and intuitive design. Particular emphasis was given to the automation of several tedious tasks, such as extraction of clusters of structures based on dihedral and Cartesian principal component analysis, secondary structure analysis, calculation and display of root-mean-square deviation (RMSD) matrices, calculation of entropy, calculation and analysis of variance–covariance matrices, calculation of the fraction of native contacts, etc. The program is free-open source software available immediately for download. © 2013 Wiley Periodicals, Inc.