Irfan Alibay - Towards MDAnalysis 3.0 | SciPy 2024

MDAnalysis is a 17-year-old open-source Python library for analyzing molecular dynamics simulations, with support for most MD engines and file formats

Key features include:

• Reading/writing multiple trajectory formats
• Analysis tools and distance calculations
• On-the-fly trajectory transformations
• Extensible architecture for custom analyses
• NumPy array-based data structures

Moving towards MDAnalysis 3.0 (2025) with focus on:

• Performance improvements through Cython/C++ optimization
• Better handling of large datasets (multi-TB)
• Improved distance calculations via vectorization
• Enhanced parallelization capabilities
• Slimmer, more maintainable codebase

New “MDAnalysis Kits” initiative:

• Similar to scikit model
• Encourages community-developed downstream packages
• Weekly testing of submitted kits
• Central registry for discovery

Community growth efforts include:

• Google Summer of Code mentorship
• Workshops and outreach programs
• User guides and documentation
• 206+ contributors to date
• Community events and meetings

Technical improvements:

• New data structures at C-level
• Enhanced interoperability with other libraries
• Improved distance calculations library
• Better periodic boundary condition handling
• GPU support for larger systems