MDAnalysis

What it is and what it does

MDAnalysis is a Python library for reading, manipulating, and analyzing molecular dynamics simulation trajectories. It abstracts away the complexity of different trajectory file formats—supporting GROMACS, Amber, NAMD, CHARMM, DL_POLY, HOOMD, LAMMPS, and others—and provides a unified interface to select atoms, extract structural data as NumPy arrays, and iterate through frames. The library is written by and for computational scientists and includes a growing collection of analysis algorithms for tasks like RMSD calculations, structural alignment, and distance analysis.

The package is mature (first released in 2012), actively maintained, and fiscally sponsored by NumFOCUS. It has a large dependency footprint (11 runtime packages including numpy, scipy, and matplotlib) and is designed for interactive exploration and scripting of simulation data. Prebuilt wheels cover recent Python versions and major platforms, making installation straightforward for most users.

Use it for:

• Load and iterate through molecular dynamics trajectories from GROMACS, Amber, or NAMD simulations to extract atomic positions and velocities.
• Select subsets of atoms (e.g., 'name OH' or 'protein and backbone') and compute structural properties like center of mass or distances.
• Perform RMSD calculations and structural alignment to compare protein conformations across trajectory frames.
• Extract time-series data (positions, forces, velocities) as NumPy arrays for downstream statistical or machine-learning analysis.
• Analyze drug–protein interactions or material properties by computing contact distances and structural metrics over simulation time.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

MDAnalysis reads and analyzes molecular dynamics simulation trajectories from many popular simulation packages, providing atom selection, structural analysis, and trajectory iteration through a Python API.

Yes. MDAnalysis is a mature, actively maintained library with broad support for simulation formats and a large user base in computational chemistry and biophysics. Install friction is moderate but manageable; the LGPLv3+ license is permissive for most use cases. No known security vulnerabilities. Install it if you work with molecular dynamics simulations and need a standard, well-documented toolkit for trajectory analysis.

Install

mdanalysis on PyPI

pip install mdanalysis

uv add mdanalysis

poetry add mdanalysis

Installing MDAnalysis

Before you install

Medium install friction: 11 runtime dependencies including numpy, scipy, matplotlib, and joblib. Prebuilt wheels available for Python 3.11–3.14 on macOS, Windows, and Linux. Actively maintained with recent commits; last release 301 days old but repository shows ongoing development.

License in practice

Licensed under LGPLv3+ with some components under LGPLv2.1+. Permissive for linking into non-free software; you may use and modify it freely, but derivative works must remain under LGPL. No restriction on closed-source applications that link to it.

Quickstart

pip install mdanalysis
import MDAnalysis as mda
u = mda.Universe('topol.tpr', 'traj.trr')
ag = u.select_atoms('name OH')
for ts in u.trajectory:
    print(ag.center_of_mass())

Verify before relying

• Performance characteristics and scalability limits for large trajectory files or systems
• Specific analysis algorithms included in MDAnalysis.analysis module beyond what the description excerpt covers
• Memory requirements and optimal hardware for typical use cases

Package facts

Evidence: mdanalysis-2.10.0-cp311-cp311-macosx_10_9_x86_64.whl; mdanalysis-2.10.0-cp311-cp311-macosx_11_0_arm64.whl; mdanalysis-2.10.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl; mdanalysis-2.10.0-cp311-cp311-win_amd64.whl; mdanalysis-2.10.0-cp312-cp312-macosx_10_13_x86_64.whl; mdanalysis-2.10.0-cp312-cp312-macosx_11_0_arm64.whl; mdanalysis-2.10.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl; mdanalysis-2.10.0-cp312-cp312-win_amd64.whl; mdanalysis-2.10.0-cp313-cp313-macosx_10_13_x86_64.whl; mdanalysis-2.10.0-cp313-cp313-macosx_11_0_arm64.whl; mdanalysis-2.10.0-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl; mdanalysis-2.10.0-cp313-cp313-win_amd64.whl; mdanalysis-2.10.0-cp314-cp314-macosx_10_13_x86_64.whl; mdanalysis-2.10.0-cp314-cp314-macosx_11_0_arm64.whl; mdanalysis-2.10.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl; mdanalysis-2.10.0-cp314-cp314-win_amd64.whl

Keywords: python, science, chemistry, biophysics, molecular-dynamics, computational-chemistry, molecular-simulation, analysis, trajectory-analysis

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