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MDAnalysis: A toolkitfor the analysis ofmolecular dynamicssimulations Naveen Michaud‐AgrawalElizabeth J. DenningThomas B. Woolf2011 год

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
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Аннотация: Abstract MDAnalysis is an object‐oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. It is written in the Python language with some performance‐critical code in C. It uses the powerful NumPy package to expose trajectory data as fast and efficient NumPy arrays. It has been tested on systems of millions of particles. Many common file formats of simulation packages including CHARMM, Gromacs, Amber, and NAMD and the Protein Data Bank format can be read and written. Atoms can be selected with a syntax similar to CHARMM's powerful selection commands. MDAnalysis enables both novice and experienced programmers to rapidly write their own analytical tools and access data stored in trajectories in an easily accessible manner that facilitates interactive explorative analysis. MDAnalysis has been tested on and works for most Unix‐based platforms such as Linux and Mac OS X. It is freely available under the GNU General Public License from http://mdanalysis.googlecode.com . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011
Год издания: 2011
Авторы: Naveen Michaud‐Agrawal, Elizabeth J. Denning, Thomas B. Woolf, Oliver Beckstein
Издательство: Wiley
Источник: Journal of Computational Chemistry
Ключевые слова: Protein Structure and Dynamics, Enzyme Structure and Function, Spectroscopy and Quantum Chemical Studies
Другие ссылки: Journal of Computational Chemistry (PDF)
Journal of Computational Chemistry (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
PubMed Central (HTML)
PubMed (HTML)