Conference site » Proceedings

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations

Richard J. Gowers
University of Manchester, Manchester, UK
University of Edinburgh, Edinburgh, UK

Max Linke
Max Planck Institut für Biophysik, Frankfurt, Germany

Jonathan Barnoud
University of Groningen, Groningen, The Netherlands

Tyler J. E. Reddy
University of Oxford, Oxford, UK

Manuel N. Melo
University of Groningen, Groningen, The Netherlands

Sean L. Seyler
Arizona State University, Tempe, Arizona, USA

Jan Domański
University of Oxford, Oxford, UK

David L. Dotson
Arizona State University, Tempe, Arizona, USA

Sébastien Buchoux
Université de Picardie Jules Verne, Amiens, France

Ian M. Kenney
Arizona State University, Tempe, Arizona, USA

Oliver Beckstein
Arizona State University, Tempe, Arizona, USA

Video: https://youtu.be/zVQGFysYDew

Abstract

MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. MD simulations of biological molecules have become an important tool to elucidate the relationship between molecular structure and physiological function. Simulations are performed with highly optimized software packages on HPC resources but most codes generate output trajectories in their own formats so that the development of new trajectory analysis algorithms is confined to specific user communities and widespread adoption and further development is delayed. MDAnalysis addresses this problem by abstracting access to the raw simulation data and presenting a uniform object-oriented Python interface to the user. It thus enables users to rapidly write code that is portable and immediately usable in virtually all biomolecular simulation communities. The user interface and modular design work equally well in complex scripted work flows, as foundations for other packages, and for interactive and rapid prototyping work in IPython / Jupyter notebooks, especially together with molecular visualization provided by nglview and time series analysis with pandas. MDAnalysis is written in Python and Cython and uses NumPy arrays for easy interoperability with the wider scientific Python ecosystem. It is widely used and forms the foundation for more specialized biomolecular simulation tools. MDAnalysis is available under the GNU General Public License v2.

Keywords

molecular dynamics simulations, science, chemistry, physics, biology

Bibtex entry

Full text PDF