MDTraj: an open-source library for analysis of molecular dynamics trajectories

MDTraj is a python library that allows users to manipulate molecular dynamics (MD) trajectories and perform a variety of analyses, including fast RMSD, solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj is the wide variety of molecular dynamics trajectory file formats which are supported, including RCSB pdb, GROMACS xtc, and trr, CHARMM / NAMD dcd, AMBER AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5."

Read, write and analyze MD trajectories with only a few lines of Python code.

Features

With MDTraj, you can:

Read and write from every MD format imaginable (pdb, xtc, trr, dcd, netcdf, mdcrd, prmtop, gsd, ...)
Run blazingly fast RMSD calculations (4x the speed of the original Theobald QCP).
Use tons of analysis functions like bonds/angles/dihedrals, hydrogen bonding identification, secondary structure assignment, NMR observables.
Use a lightweight API, with a focus on speed and vectorized operations.

For details, see the documentation. To get involved, take a look at the GitHub issue tracker and/or the Discussions section.

Citation

MDTraj is research software. If you make use of MDTraj in scientific publications, please cite it. The BibTeX reference is

@article{McGibbon2015MDTraj,
    author = {McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hern{\'a}ndez, Carlos X.  and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.},
    title = {MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories},
    journal = {Biophysical Journal},
    volume = {109},
    number = {8},
    pages = {1528 -- 1532},
    year = {2015},
    doi = {10.1016/j.bpj.2015.08.015}
}

License

GNU LGPL version 2.1, or at your option a later version of the license. Various sub-portions of this library may be independently distributed under different licenses. See those files for their specific terms.

Project Status

MDTraj is actively maintained by community members and representatives from Folding@Home, The Molecular Sciences Software Institute, and Open Force Field Initiative. We welcome new users and contributors!

If you are interested in contributing, please check out the repository issue tracker. For feature ideas or general questions, please post in the repository discussions.

Metadata

Release files for mdtraj 1.11.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for mdtraj 1.11.2
File	Size	Uploaded
mdtraj-1.11.2.tar.gz	2.9 MB	Oct 5, 2026	Details

Built distributions (wheels)

Table of built distributions (wheels) for mdtraj 1.11.2
File	Interpreter	ABI	Platform	Reset
mdtraj-1.11.2-cp315-cp315-win_amd64.whl 4.2 MB Oct 14, 2026	CPython 3.15	CPython 3.15	Windows x86-64	Details
mdtraj-1.11.2-cp315-cp315-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 11.5 MB Oct 12, 2026	CPython 3.15	CPython 3.15	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
mdtraj-1.11.2-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 11.2 MB Oct 13, 2026	CPython 3.15	CPython 3.15	Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64	Details
mdtraj-1.11.2-cp315-cp315-macosx_11_0_x86_64.whl 4.2 MB Oct 13, 2026	CPython 3.15	CPython 3.15	macOS 11.0+ x86-64	Details
mdtraj-1.11.2-cp315-cp315-macosx_11_0_arm64.whl 4.1 MB Oct 13, 2026	CPython 3.15	CPython 3.15	macOS 11.0+ ARM64	Details
mdtraj-1.11.2-cp314-cp314-win_amd64.whl 4.5 MB Oct 5, 2026	CPython 3.14	CPython 3.14	Windows x86-64	Details
mdtraj-1.11.2-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 11.5 MB Oct 5, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
mdtraj-1.11.2-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 11.3 MB Oct 5, 2026	CPython 3.14	CPython 3.14	Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64	Details
mdtraj-1.11.2-cp314-cp314-macosx_10_15_universal2.whl 5.4 MB Oct 5, 2026	CPython 3.14	CPython 3.14	macOS 10.15+ universal2 (ARM64, x86-64)	Details
mdtraj-1.11.2-cp313-cp313-win_amd64.whl 4.4 MB Oct 5, 2026	CPython 3.13	CPython 3.13	Windows x86-64	Details
mdtraj-1.11.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 11.6 MB Oct 5, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64	Details
mdtraj-1.11.2-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 11.3 MB Oct 5, 2026	CPython 3.13	CPython 3.13	Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64	Details
mdtraj-1.11.2-cp313-cp313-macosx_10_13_universal2.whl 5.4 MB Oct 5, 2026	CPython 3.13	CPython 3.13	macOS 10.13+ universal2 (ARM64, x86-64)	Details
mdtraj-1.11.2-cp312-cp312-win_amd64.whl 4.4 MB Oct 5, 2026	CPython 3.12	CPython 3.12	Windows x86-64	Details
mdtraj-1.11.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 11.6 MB Oct 5, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64	Details
mdtraj-1.11.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 11.3 MB Oct 5, 2026	CPython 3.12	CPython 3.12	Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64	Details
mdtraj-1.11.2-cp312-cp312-macosx_10_13_universal2.whl 5.4 MB Oct 5, 2026	CPython 3.12	CPython 3.12	macOS 10.13+ universal2 (ARM64, x86-64)	Details

Total release size: 136.3 MB

Release files / mdtraj-1.11.2.tar.gz

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Release files / mdtraj-1.11.2-cp315-cp315-win_amd64.whl

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Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

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Release files / mdtraj-1.11.2-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

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Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

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Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

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Release files / mdtraj-1.11.2-cp313-cp313-win_amd64.whl

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Size	4.4 MB
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Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

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Publishing configuration: github.com/mdtraj/mdtraj/blob/ffd10889bbcff43abdf7ffd688f10e9d7baa9139/.github/workflows/build.yaml
Publishing logs: github.com/mdtraj/mdtraj/actions/runs/37335862665/attempts/1

Artifact

Subject: mdtraj-1.11.2-cp313-cp313-macosx_10_13_universal2.whl
SHA-256 checksum: 00416ccb4705a2b754cccb790eaebfdcf5557c5e3ae6913ebd2bc32b1a2c2a9d Verifying attestations

Release files / mdtraj-1.11.2-cp312-cp312-win_amd64.whl

Download URL	mdtraj-1.11.2-cp312-cp312-win_amd64.whl
Size	4.4 MB
Tags	CPython 3.12 Windows x86-64
SHA-256 checksum How to use checksums	`76c3bb211c44e731de7f3e434875ac537db97b3ebb141c3f59907586488a9f36`
BLAKE2b-256 checksum How to use checksums	`6c349bd74ffa1d485c4ec4870ea6b77add135e1b71559332db23d96495de6605`
Upload date	Oct 5, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/mdtraj/mdtraj
Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

Workflow

Publishing configuration: github.com/mdtraj/mdtraj/blob/ffd10889bbcff43abdf7ffd688f10e9d7baa9139/.github/workflows/build.yaml
Publishing logs: github.com/mdtraj/mdtraj/actions/runs/37335862665/attempts/1

Artifact

Subject: mdtraj-1.11.2-cp312-cp312-win_amd64.whl
SHA-256 checksum: 76c3bb211c44e731de7f3e434875ac537db97b3ebb141c3f59907586488a9f36 Verifying attestations

Release files / mdtraj-1.11.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

Download URL	mdtraj-1.11.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
Size	11.6 MB
Tags	CPython 3.12 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64
SHA-256 checksum How to use checksums	`a983325c237ff6791716a984c886265c8c2a79c1c83e5aaa2b634a7c0311b791`
BLAKE2b-256 checksum How to use checksums	`be49477b9ceff3dd386f12cbfe3a67a5e707d70f64e3532ef3238fd97b47dc55`
Upload date	Oct 5, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/mdtraj/mdtraj
Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

Workflow

Publishing configuration: github.com/mdtraj/mdtraj/blob/ffd10889bbcff43abdf7ffd688f10e9d7baa9139/.github/workflows/build.yaml
Publishing logs: github.com/mdtraj/mdtraj/actions/runs/37335862665/attempts/1

Artifact

Subject: mdtraj-1.11.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
SHA-256 checksum: a983325c237ff6791716a984c886265c8c2a79c1c83e5aaa2b634a7c0311b791 Verifying attestations

Release files / mdtraj-1.11.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl

Download URL	mdtraj-1.11.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
Size	11.3 MB
Tags	CPython 3.12 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64
SHA-256 checksum How to use checksums	`efc6447c05d149affab4b253166115c65257459c105452cb27f18f126d305c1a`
BLAKE2b-256 checksum How to use checksums	`697bb24c473318ce0ec6a4d61ec0193aced7ae7df2b3ad2cc42b29093027c1bf`
Upload date	Oct 5, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/mdtraj/mdtraj
Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

Workflow

Publishing configuration: github.com/mdtraj/mdtraj/blob/ffd10889bbcff43abdf7ffd688f10e9d7baa9139/.github/workflows/build.yaml
Publishing logs: github.com/mdtraj/mdtraj/actions/runs/37335862665/attempts/1

Artifact

Subject: mdtraj-1.11.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
SHA-256 checksum: efc6447c05d149affab4b253166115c65257459c105452cb27f18f126d305c1a Verifying attestations

Release files / mdtraj-1.11.2-cp312-cp312-macosx_10_13_universal2.whl

Download URL	mdtraj-1.11.2-cp312-cp312-macosx_10_13_universal2.whl
Size	5.4 MB
Tags	CPython 3.12 macOS 10.13+ universal2 (ARM64, x86-64)
SHA-256 checksum How to use checksums	`407b192f6cac20664bd574052031c9e3fa03bc3002d6957d262c1a854dfd2402`
BLAKE2b-256 checksum How to use checksums	`5b6ddcac79537deb978229f491ffa2d1d2a63e77990fbe60181020c23ec22ce0`
Upload date	Oct 5, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	Yes
Uploaded via	`twine/7.0.0 CPython/3.13.14`

Provenance

Identity

Publishing platform: GitHub Actions
Publishing repository: github.com/mdtraj/mdtraj
Publishing commit: github.com/mdtraj/mdtraj/tree/ffd10889bbcff43abdf7ffd688f10e9d7baa9139

Workflow

Publishing configuration: github.com/mdtraj/mdtraj/blob/ffd10889bbcff43abdf7ffd688f10e9d7baa9139/.github/workflows/build.yaml
Publishing logs: github.com/mdtraj/mdtraj/actions/runs/37335862665/attempts/1

Artifact

Subject: mdtraj-1.11.2-cp312-cp312-macosx_10_13_universal2.whl
SHA-256 checksum: 407b192f6cac20664bd574052031c9e3fa03bc3002d6957d262c1a854dfd2402 Verifying attestations