MDAnalysis / mdanalysis

================================ MDAnalysis Repository README ================================ |numfocus| |build| |cron| |cirruscron| |linters| |cov| |docs| |devdocs| |discussions| |pypi| |anaconda| |asv| 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 _ and _. MDAnalysis also includes widely used analysis algorithms in the _ module. .. _numfocus-fiscal-sponsor-attribution: The MDAnalysis project uses an _ and is fiscally sponsored by _. Consider making a _ to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs. .. image:: https://www.mdanalysis.org/public/images/numfocus-sponsored-small.png :alt: NumFOCUS (Fiscally Sponsored Project) :target: https://numfocus.org/project/mdanalysis :align: center This project is bound by a _. |powered_by_MDA| If you use MDAnalysis_ in your project consider letting your users and the world know about it by displaying the MDAnalysis_ badge! _ is available for different markups. Example analysis script ======================= .. code:: python 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 _ and might want to look at our videos_, in which core developers explain various aspects of MDAnalysis. **All users** should read the _. **Developers** may also want to refer to the _. A growing number of _ 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 _. **Source code** is hosted in a git repository at https://github.com/MDAnalysis/mdanalysis and is packaged under the GNU Lesser General Public License, version 3 or any later version (LGPLv3+). Individual source code components are provided under the GNU Lesser General Public License, version 2.1 or any later version (LGPLv2.1+). Please see the file LICENSE_ for more information. Contributing ============ Please report **bugs** or **enhancement requests** through the _. Questions can also be asked on _. If you are a **new developer** who would like to start contributing to MDAnalysis get in touch on _. To set up a development environment and run the test suite read the _. 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: _ • 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: _ For citations of included algorithms and sub-modules please see the references_. .. _NumFOCUS: https://numfocus.org/ .. _open governance model: https://www.mdanalysis.org/pages/governance/ .. _tax-deductible donation: https://numfocus.org/donate-to-mdanalysis .. _ : https://www.mdanalysis.org/conduct/ .. _trajectory formats: https://docs.mdanalysis.org/documentation_pages/coordinates/init.html#id1 .. _topology formats: https://docs.mdanalysis.org/documentation_pages/topology/init.html#supported-topology-formats .. _MDAnalysis: https://www.mdanalysis.org .. _LICENSE: https://github.com/MDAnalysis/mdanalysis/blob/develop/LICENSE .. _ : https://www.mdanalysis.org/pages/installation_quick_start/ .. _ : https://docs.mdanalysis.org/documentation_pages/analysis_modules.html .. _ : https://userguide.mdanalysis.org/examples/README.html .. _ : https://www.mdanalysis.org/pages/learning_MDAnalysis/#videos .. _ : https://userguide.mdanalysis.org/examples/quickstart.html .. _ : https://userguide.mdanalysis.org .. _ : https://docs.mdanalysis.org .. _ : https://github.com/mdanalysis/mdanalysis/issues .. _ : https://github.com/MDAnalysis/mdanalysis/discussions .. _ : https://userguide.mdanalysis.org/contributing.html .. _ : https://dx.doi.org/10.1002/jcc.21787 .. _ : https://doi.org/10.25080/Majora-629e541a-00e .. _references: https://docs.mdanalysis.org/documentation_pages/references.html .. _Embedding code: https://www.mdanalysis.org/pages/citations/#powered-by-mdanalysis .. |docs| image:: https://img.shields.io/badge/docs-latest-brightgreen.svg :alt: Documentation (latest release) :target: https://docs.mdanalysis.org .. |devdocs| image:: https://img.shields.io/badge/docs-development-yellow.svg :alt: Documentation (development version) :target: https://docs.mdanalysis.org/dev .. |numfocus| image:: https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A :alt: Powered by NumFOCUS :target: https://www.numfocus.org/ .. |build| image:: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml/badge.svg :alt: Github Actions Build Status :target: https://github.com/MDAnalysis/mdanalysis/actions/workflows/gh-ci.yaml .. |cron| image:: https://github.com/MDAnalysis/mdanalysis/actions/wo…