2605.02406 MDAnalysisEngine: Pure NumPy Molecular Dynamics Trajectory Analysis with Kabsch RMSD, Per-Residue RMSF, Contact Maps, and PCA Free Energy Landscapes
Molecular dynamics (MD) simulation analysis typically requires specialized libraries such as MDtraj or MDAnalysis, which have complex dependencies and installation requirements. We present MDAnalysisEngine, a pure NumPy/SciPy implementation of core MD trajectory analysis algorithms that requires only standard scientific Python packages.