3590117

MDAnalysis 2.0 and beyond: Extensible and interoperable simulation analyses

Date
August 23, 2021

As computing power advances, molecular dynamics simulations have become increasingly complex. Correspondingly, analysis workflows must evolve to extract the simulation features required for scientific interpretation. We present MDAnalysis (https://www.mdanalysis.org), a free open-source Python library for extensible molecular simulation analysis with over 120 contributors and 16 years of continued development. MDAnalysis offers a variety of built-in analysis methods, efficient routines for trajectory manipulation and system preparation, and supports over 40 file formats from popular simulation packages. Here we describe the core aspects of MDAnalysis and how it can be leveraged to explore simulation data, focusing specifically on recently implemented features that address modern simulation analysis challenges: software interoperability and the efficient handling of large datasets.

We introduce our new "converter" framework, our solution to the software interoperability problem. Here, data can be converted to and from Python objects from other popular simulation and analysis packages such as ParmEd and RDKit. This enables immediate interoperability at the code level, without the need for intermediary files. We also detail our progress in using multi-core parallelism to routinely process large-scale datasets. Finally, we discuss the future directions for the MDAnalysis library, particularly challenges and strategies for enabling users to develop reproducible analysis tools and packages.

Presenter

Speaker Image for Irfan Alibay
Postdoctoral Research Associate, The University of Oxford

Speakers

Speaker Image for Oliver Beckstein
Associate Professor, Arizona State University
Speaker Image for Richard Gowers
Senior software engineer, NextMove Software
Speaker Image for Micaela Matta
Lecturer (Assistant Professor), University of Liverpool School of Physical Sciences

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