MDTraj

MDTraj is an open-source Python library designed for the analysis of molecular dynamics trajectory data. It provides tools to read, manipulate, and analyze trajectory files produced by common MD packages, and it emphasizes efficient, geometry-focused computation on large datasets. MDTraj is suitable for researchers working with protein, nucleic acid, and small-molecule simulations, and it supports interoperability with multiple simulation ecosystems.

The library centers on a Trajectory object, which pairs a topology description with a time series of coordinates. The topology encodes atoms, residues, chains, and bonds, enabling meaningful geometric measurements. MDTraj supports reading and writing a wide range of trajectory formats, including DCD, XTC, TRR, NetCDF, PDB, GRO, and others, and it provides a simple API for selecting atom groups and aligning trajectories to reference structures.

Core analytical capabilities include computation of distances, angles, and dihedrals, as well as global measures such as root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF). The library also offers tools for selecting subsets of atoms, computing pairwise contacts, and performing more specialized analyses such as hydrogen bonds and native contact maps. These capabilities enable researchers to quantify structural changes, compare conformations, and extract meaningful statistics from simulation data.

MDTraj emphasizes performance through a C++ core with Python bindings and relies on NumPy for data handling. Typical workflows involve loading trajectories, aligning to a reference, calculating metrics of interest, and exporting results for further analysis or visualization. The project serves as a lightweight, versatile tool for trajectory analysis within the broader MD simulation ecosystem, and it is maintained with documentation and a community of users.