github.com/mdtraj/mdtraj ↗
An open library for the analysis of molecular dynamics trajectories
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Contributors
95
Lines of Code
7,417
From
2012-11-08
To
2021-02-02
About mdtraj/mdtraj
MDTraj is a Python library for reading, writing, and analyzing molecular dynamics simulation trajectories. It supports an extensive range of file formats including PDB, GROMACS (xtc and trr), CHARMM/NAMD (dcd), AMBER (NetCDF and mdcrd), TINKER (arc), and HDF5, making it a versatile tool for researchers working with different simulation software packages.
The library provides optimized implementations of common analysis tasks in computational chemistry, including RMSD calculations that are significantly faster than standard implementations, hydrogen bonding identification, secondary structure assignment, and geometric analysis of bonds, angles, and dihedral angles. The API emphasizes speed and vectorized operations to handle large trajectory datasets efficiently, allowing users to accomplish complex analyses with minimal code.
MDTraj is actively maintained by a community including contributors from Folding@Home, the Molecular Sciences Software Institute, and the Open Force Field Initiative. The project is distributed under the GNU LGPL version 2.1 and welcomes contributions from the scientific computing community. It serves researchers in computational biology, chemistry, and related fields who need robust tools for analyzing molecular dynamics simulations.