MDAnalysis - Molecular Dynamics Analysis

Python library for reading, writing, and analyzing molecular dynamics trajectories and structural files.

When to Use

• Loading MD trajectories (DCD, XTC, TRR, NetCDF, etc.)
• RMSD and RMSF calculations
• Distance, angle, and dihedral analysis
• Atom selections (VMD-like syntax)
• Hydrogen bond analysis
• Solvent Accessible Surface Area (SASA)
• Protein secondary structure analysis
• Membrane system analysis
• Water/ion distribution analysis
• Trajectory alignment and fitting
• Custom trajectory analysis
• Converting between file formats