Sep 9, 2014

MDTraj: a modern, open library for the analysis of molecular dynamics trajectories

BioRxiv : the Preprint Server for Biology
Robert T McGibbonVijay S Pande

Abstract

Summary: MDTraj is a modern, lightweight and efficient software package for analyzing molecular dynamics simulations. MDTraj reads trajectory data from a wide variety of commonly used formats. It provides a large number of trajectory analysis capabilities including RMSD, DSSP secondary structure assignment and the extraction of common order parameters. The package has a strong focus on interoperability with the wider scientific Python ecosystem, bridging the gap between molecular dynamics data and the rapidly-growing collection of industry-standard statistical analysis and visualization tools in Python. Availability: Package downloads, detailed examples and full documentation are available at <http://mdtraj.org>. The source code is distributed under the GNU Lesser General Public License at <https://github.com/simtk/mdtraj>.

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Mentioned in this Paper

Computer Software
Molecular Dynamics
Extraction
Public Entity
Structure
Simulation
Analysis
Statistical Analysis

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