MDAnalysis/mdanalysis

Health v2 · maintenance only

Flags: no_license

Adoption not part of the score

1637 stars · 858 forks observed · 2026-08-28

What it is AI-extracted, prompt v1, taxonomy v1, 2026-08-30, confidence not recorded

MDAnalysis is an open-source Python library for analyzing molecular dynamics simulations of many-body systems at the molecular scale. It reads and writes trajectory and topology formats from popular simulation packages like GROMACS, Amber, NAMD, and LAMMPS, exposing atomic data as NumPy arrays with built-in analysis algorithms.

Use cases

• analyze molecular dynamics trajectories in python
• compute RMSD and structural alignment of proteins
• read GROMACS or Amber trajectory files
• calculate center of mass and distances of atom groups
• select subsets of atoms from simulation topologies
• analyze drug-protein interactions from MD simulations
• convert between molecular simulation file formats

When to choose

• you need to analyze MD simulation trajectories from common packages in Python
• you want NumPy-based access to atomic coordinates, velocities, and forces
• you need established analysis algorithms like RMSD, contacts, or distances
• you work with biomolecular or materials simulation data

When to avoid

• you need to run or set up simulations rather than analyze them
• you need a GUI-based visual analysis tool
• your data is not molecular simulation trajectory or topology data

Facets

library · maturity stable

data-science parser math simulation chemistry bioinformatics data-science simulation python cross-platform molecular-dynamics trajectory-analysis computational-chemistry numpy scientific-computing gromacs pdb science

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markdown · JSON · MCP: product_card(name="MDAnalysis/mdanalysis")