An object-oriented toolkit to analyze molecular dynamics trajectories.

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for IAlibay from gravatar.com IAlibay Avatar for lilyminium from gravatar.com lilyminium Avatar for Oliver.Beckstein from gravatar.com Oliver.Beckstein Avatar for richard.j.gowers from gravatar.com richard.j.gowers

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v2 or later (GPLv2+) (========================================================================== Licenses of components of...)
  • Author: MDAnalysis Development Team
  • Maintainer: MDAnalysis Core Developers
  • Tags python, science, chemistry, biophysics, molecular-dynamics, computational-chemistry, molecular-simulation, analysis, trajectory-analysis
  • Requires: Python >=3.8
Classifiers

Project description

Powered by NumFOCUS Github Actions Build Status Github Actions Cron Job Status Travis CI Build Status Coverage Status

Documentation (latest release) Documentation (development version) User Google Group Developer Google Group Anaconda My Binder ASV Benchmarks

MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists.

It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported trajectory formats and topology formats. MDAnalysis also includes widely used analysis algorithms in the MDAnalysis.analysis module.

The MDAnalysis project uses an open governance model and is fiscally sponsored by NumFOCUS. Consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

NumFOCUS (Fiscally Sponsored Project)

This project is bound by a Code of Conduct.

Powered by MDAnalysis

If you use MDAnalysis in your project consider lettting your users and the world know about it by displaying the MDAnalysis badge! Embedding code is available for different markups.

Example analysis script

import MDAnalysis as mda

# Load simulation results with a single line
u = mda.Universe('topol.tpr','traj.trr')

# Select atoms
ag = u.select_atoms('name OH')

# Atom data made available as Numpy arrays
ag.positions
ag.velocities
ag.forces

# Iterate through trajectories
for ts in u.trajectory:
    print(ag.center_of_mass())

Documentation

New users should read the Quickstart Guide and might want to look at our videos, in which core developers explain various aspects of MDAnalysis.

All users should read the User Guide.

Developers may also want to refer to the MDAnalysis API docs.

A growing number of tutorials are available that explain how to conduct RMSD calculations, structural alignment, distance and contact analysis, and many more.

Installation and availability

The latest release can be installed via pip or conda as described in the Installation Quick Start.

Source code is hosted in a git repository at https://github.com/MDAnalysis/mdanalysis and is available under the GNU General Public License, version 2 (see the file LICENSE).

Contributing

Please report bugs or enhancement requests through the Issue Tracker. Questions can also be asked on the user mailing list.

If you are a new developer who would like to start contributing to MDAnalysis get in touch on the developer mailing list. To set up a development environment and run the test suite read the developer guide.

Citation

When using MDAnalysis in published work, please cite the following two papers:

  • R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. doi:10.25080/Majora-629e541a-00e

  • N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319–2327. doi:10.1002/jcc.21787

For citations of included algorithms and sub-modules please see the references.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for IAlibay from gravatar.com IAlibay Avatar for lilyminium from gravatar.com lilyminium Avatar for Oliver.Beckstein from gravatar.com Oliver.Beckstein Avatar for richard.j.gowers from gravatar.com richard.j.gowers

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU General Public License v2 or later (GPLv2+) (========================================================================== Licenses of components of...)
  • Author: MDAnalysis Development Team
  • Maintainer: MDAnalysis Core Developers
  • Tags python, science, chemistry, biophysics, molecular-dynamics, computational-chemistry, molecular-simulation, analysis, trajectory-analysis
  • Requires: Python >=3.8
Classifiers

Release history Release notifications | RSS feed

2.7.0

2.6.1

2.6.0

2.5.0

2.5.0.dev0 pre-release yanked

Reason this release was yanked:

unintended release

2.4.3

This version

2.4.2

2.4.1

2.4.0 yanked

Reason this release was yanked:

bad biopython pin

2.3.0

2.2.0

2.1.0

2.0.0

2.0.0b0 pre-release

1.1.1

1.1.0 yanked

Reason this release was yanked:

Bad SOURCES.txt

1.0.1

1.0.0

0.20.1

0.20.0

0.19.2

0.19.1

0.19.0

0.18.0

0.17.0

0.16.2

0.16.1

0.16.0

0.15.0

0.14.0

0.13.0

0.12.1

0.11.0

0.10.0

0.9.2

0.9.1

0.9.0

0.9.0-dev pre-release

0.8.1

0.8.1rc1 pre-release

0.8.0

0.8.0rc4 pre-release

0.8.0rc2 pre-release

0.7.7

0.7.7-rc1 pre-release

0.7.6

0.7.5.1

0.7.5

0.7.4

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

MDAnalysis-2.4.2.tar.gz (3.7 MB view details)

Uploaded Source

Built Distributions

MDAnalysis-2.4.2-cp311-cp311-win_amd64.whl (3.2 MB view details)

Uploaded CPython 3.11 Windows x86-64

MDAnalysis-2.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.2 MB view details)

Uploaded CPython 3.11 manylinux: glibc 2.17+ x86-64

MDAnalysis-2.4.2-cp311-cp311-macosx_10_9_x86_64.whl (3.4 MB view details)

Uploaded CPython 3.11 macOS 10.9+ x86-64

MDAnalysis-2.4.2-cp310-cp310-win_amd64.whl (3.2 MB view details)

Uploaded CPython 3.10 Windows x86-64

MDAnalysis-2.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.0 MB view details)

Uploaded CPython 3.10 manylinux: glibc 2.17+ x86-64

MDAnalysis-2.4.2-cp310-cp310-macosx_10_9_x86_64.whl (3.4 MB view details)

Uploaded CPython 3.10 macOS 10.9+ x86-64

MDAnalysis-2.4.2-cp39-cp39-win_amd64.whl (3.2 MB view details)

Uploaded CPython 3.9 Windows x86-64

MDAnalysis-2.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.1 MB view details)

Uploaded CPython 3.9 manylinux: glibc 2.17+ x86-64

MDAnalysis-2.4.2-cp39-cp39-macosx_10_9_x86_64.whl (3.4 MB view details)

Uploaded CPython 3.9 macOS 10.9+ x86-64

MDAnalysis-2.4.2-cp38-cp38-win_amd64.whl (3.2 MB view details)

Uploaded CPython 3.8 Windows x86-64

MDAnalysis-2.4.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.1 MB view details)

Uploaded CPython 3.8 manylinux: glibc 2.17+ x86-64

MDAnalysis-2.4.2-cp38-cp38-macosx_10_9_x86_64.whl (3.4 MB view details)

Uploaded CPython 3.8 macOS 10.9+ x86-64

File details

Details for the file MDAnalysis-2.4.2.tar.gz.

File metadata

  • Download URL: MDAnalysis-2.4.2.tar.gz
  • Upload date:
  • Size: 3.7 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.9.16

File hashes

Hashes for MDAnalysis-2.4.2.tar.gz
Algorithm Hash digest
SHA256 ae2ee5627391e73f74eaa3c547af3ec6ab8b040d27dedffe3a7ece8e0cd27636
MD5 8945fc2fd883a44d982e61c321d6311d
BLAKE2b-256 7d6bf0ea2ab44ed0a2448737d779e02d3ae719c186dc9e3ce4cd0d75b4026dcc

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp311-cp311-win_amd64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp311-cp311-win_amd64.whl
Algorithm Hash digest
SHA256 97587b4a48a702964814446520c4be761d9319997c103b6739df9c21581367c7
MD5 00a9a65c6f7cb50f6210338347847281
BLAKE2b-256 8b65c72765a2a6c73b8e03e114cf7e1661c28df3049adc42e8c75838b48ca083

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 0b95d0fb6903d730575a2dac3cce726fdc18b12e39326686ac2b0e0e08c813b5
MD5 c80ec6857ad6a399cafdc4a449ff220a
BLAKE2b-256 ee4020322a888419cc4aeaafa552c51c97c666a46e69c0d130dc5744ec04ae58

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp311-cp311-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp311-cp311-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 579fba5fadd8632618d3e60452eb1b682447605900de79193ab92133d4f5aced
MD5 d73e06b295d2a923906337810c5a0bb1
BLAKE2b-256 f1347eedce6129f71fa38fbf9d7fe3a8f366ddee3142afb07113598bf2b66d81

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp310-cp310-win_amd64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp310-cp310-win_amd64.whl
Algorithm Hash digest
SHA256 d4541984e4e1413595c5ea69c3ba8d302890f581113db75cddf1e987bae72b87
MD5 0b5222132880eb6f65351d34184d2980
BLAKE2b-256 7374abcb7c91e47f350db0268c2058f079c937bb2f337d73b62ca3b8dea4642e

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 cbf0987b8fc767ec07e694b9b8d91a82b6ef81b334460241871a4bbbd871512a
MD5 666157b502bd7161a51c0538694ed4e7
BLAKE2b-256 69c73dfe97658982390bbf93cf97f4aabb22025d2956bcd82b410e8c1831dfac

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp310-cp310-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 c1ea28219f39bb5acb3f71292421f2a4edcd6774178f751e6ef0b5c2552bbefe
MD5 8b220f8991ff24b66f5bcae67633c439
BLAKE2b-256 39ae52d836a64c4094794580daf0d2692fa95d244be6321fa17e6d45fe35f621

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp39-cp39-win_amd64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp39-cp39-win_amd64.whl
Algorithm Hash digest
SHA256 e823216bb54b84ca2605ec00108644d1106cf2f351c537cdb379e83f07eed597
MD5 e1b6b3892fe9f6a4c42be577dc63e706
BLAKE2b-256 8937ee29c83d622e3d55a2e2936d70cf3f3d74beaf28d5d5747385e2f9149ec8

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 a947b401d722337c0f05bf76f5131e37e44e7af62bbbaa3f93f00f7ccd5c71d9
MD5 24ae7ff203d21640d94ce6ded0ef44da
BLAKE2b-256 19cc840974bc7109839cdef50cc049336cefb2a4acc44f68913eec5f0d4db458

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp39-cp39-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 d2eb25fe13a188223d41c63470e19d55a88149a278de5b1eb49be0b81e70fc79
MD5 0a68558c188410f1b986a6ceb56cb4cb
BLAKE2b-256 899a8e6cdd8c6da04926bbaea76877b9b17082b77db742a82074b2c6dfb85e99

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp38-cp38-win_amd64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp38-cp38-win_amd64.whl
Algorithm Hash digest
SHA256 b407456f2376489868a38edf7f0d8495b5c4c4076996de5b37442f3d6d12e340
MD5 1bc9169cc092e6989d53bf3ba9c72dce
BLAKE2b-256 447f4e2ae6b5207f9782cfff053f3939433c62ef97e624bf8a71c07411d015e9

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm Hash digest
SHA256 caac5fe6f328280535168afebc584a758e564a840ff6d57e5bdeab7e4bceb7f3
MD5 d87c2c098e2c94dd4ac7f5764b501284
BLAKE2b-256 83841fa84dc9f427b8200444b1921eaf6739d9309203ffe8851a0c0e9236acb7

See more details on using hashes here.

Provenance

File details

Details for the file MDAnalysis-2.4.2-cp38-cp38-macosx_10_9_x86_64.whl.

File metadata

File hashes

Hashes for MDAnalysis-2.4.2-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm Hash digest
SHA256 218f20193da0c2aa585c9182cf683f0be86d79133e53ead2377264e8c30feace
MD5 700d002ac1bc3e4f3723584afab6a647
BLAKE2b-256 57eb504c7f70f9d10d54ce9227df3c71b128b7a15945c525ad1604a99e654973

See more details on using hashes here.

Provenance

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page