{"id":19339487,"url":"https://github.com/becksteinlab/gromacswrapper","last_synced_at":"2025-04-08T00:37:22.317Z","repository":{"id":39953471,"uuid":"597114","full_name":"Becksteinlab/GromacsWrapper","owner":"Becksteinlab","description":"GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).","archived":false,"fork":false,"pushed_at":"2024-10-07T16:40:05.000Z","size":12451,"stargazers_count":173,"open_issues_count":15,"forks_count":55,"subscribers_count":11,"default_branch":"main","last_synced_at":"2025-03-31T23:34:12.734Z","etag":null,"topics":["gromacs","gromacswrapper","molecular-dynamics","python","science"],"latest_commit_sha":null,"homepage":"https://gromacswrapper.readthedocs.org","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Becksteinlab.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGES","contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":"AUTHORS","dei":null,"publiccode":null,"codemeta":null}},"created_at":"2010-04-06T14:08:26.000Z","updated_at":"2025-02-24T19:47:50.000Z","dependencies_parsed_at":"2023-11-15T08:27:45.551Z","dependency_job_id":"3424a311-4176-47e8-9c53-5e4c9d33a8f3","html_url":"https://github.com/Becksteinlab/GromacsWrapper","commit_stats":{"total_commits":1060,"total_committers":25,"mean_commits":42.4,"dds":"0.28490566037735854","last_synced_commit":"1001a09237d1f5e475c8112a51cf964c890217a0"},"previous_names":[],"tags_count":32,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FGromacsWrapper","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FGromacsWrapper/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FGromacsWrapper/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Becksteinlab%2FGromacsWrapper/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Becksteinlab","download_url":"https://codeload.github.com/Becksteinlab/GromacsWrapper/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247755560,"owners_count":20990620,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["gromacs","gromacswrapper","molecular-dynamics","python","science"],"created_at":"2024-11-10T03:22:26.054Z","updated_at":"2025-04-08T00:37:22.291Z","avatar_url":"https://github.com/Becksteinlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":".. -*- mode: rst, coding: utf-8 -*-\n.. The whole GromacsWrapper package is Copyright (c) 2009-2018 Oliver\n.. Beckstein and AUTHORS except where noted otherwise.\n\n\n========================\n README: GromacsWrapper\n========================\n\n|build| |cov| |docs| |zenodo| |black| |PRsWelcome| |anaconda|\n\nA primitive Python wrapper around the Gromacs_ tools. The library is\ntested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x,\n2023.x, 2024.x (and 5.x and 2016.x should also work). It supports\nPython 3.9--3.12 on Linux and macOS.\n\nGromacsWrapper also provides a small library (cook book) of often-used\nrecipes and helper functions to set up MD simulations.\n\n`Documentation`_ is mostly provided through the python doc strings and\navailable at https://gromacswrapper.readthedocs.org for recent releases.\n\nThe source code is available in the `GromacsWrapper git repository`_.\n\nPlease be aware that this software is only minimally maintained and it\nmost definitely contains bugs. It is *your* responsibility to ensure\nthat you are running simulations with sensible parameters.\n\n.. _Gromacs: http://www.gromacs.org\n.. _Documentation: \n   https://gromacswrapper.readthedocs.org/en/latest/\n.. _GromacsWrapper git repository:\n   https://github.com/Becksteinlab/GromacsWrapper\n.. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=main\n   :target: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml\n   :alt: Build Status\t     \n.. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/graph/badge.svg?token=LvbLZ49wxN\n   :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper\n   :alt: Code Coverage\n.. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg\n   :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper\n   :alt: Latest release on zenodo (with DOI)\n.. |docs| image:: https://readthedocs.org/projects/gromacswrapper/badge/?version=latest\n   :target: https://gromacswrapper.readthedocs.org/en/latest/?badge=latest\n   :alt: Documentation\n.. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg\n   :target: http://makeapullrequest.com\n   :alt: PRs Welcome!\t \n.. |anaconda| image:: https://anaconda.org/conda-forge/gromacswrapper/badges/version.svg\n   :target: https://anaconda.org/conda-forge/gromacswrapper\n   :alt: Anaconda.org package\n.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg\n   :target: https://github.com/psf/black\t \n   :alt: black   \n\n\t \n\t \nQuick Start\n===========\n\nGiven a PDB file ``1iee.pdb``, set up and run a simple simulation (assuming\nyou have all other input files at hand such as the MDP files)::\n\n  \u003e\u003e\u003e import gromacs\n  \u003e\u003e\u003e print(gromacs.release)\n  2018.2\n  \u003e\u003e\u003e help(gromacs.pdb2gmx)\n  DESCRIPTION\n\n  gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,\n  adds hydrogens to the molecules and generates coordinates in GROMACS\n  ...\n  ...\n  OPTIONS\n\n  Options to specify input files:\n\n  -f      [\u003c.gro/.g96/...\u003e]  (eiwit.pdb)\n            Structure file: gro g96 pdb brk ent esp tpr\n  ...\n  ...\n  \u003e\u003e\u003e gromacs.pdb2gmx(f=\"1iee.pdb\", o=\"protein.gro\", p=\"topol.top\",\n  ...                 ff=\"oplsaa\", water=\"tip4p\")\n  \u003e\u003e\u003e gromacs.editconf(f=\"protein.gro\", o=\"boxed.gro\",\n  ...                  bt=\"dodecahedron\", d=1.5, princ=True,\n  ...                  input=\"Protein\")\n  \u003e\u003e\u003e gromacs.solvate(cp=\"boxed.gro\", cs=\"tip4p\", p=\"topol.top\",\n  ...                 o=\"solvated.gro\")\n  \u003e\u003e\u003e gromacs.grompp(f=\"emin.mdp\", c=\"solvated.gro\", p=\"topol.top\",\n  ...                o=\"emin.tpr\")\n  \u003e\u003e\u003e gromacs.mdrun(v=True, deffnm=\"emin\")\n  \u003e\u003e\u003e gromacs.grompp(f=\"md.mdp\", c=\"emin.gro\", p=\"topol.top\", o=\"md.tpr\")\n  \u003e\u003e\u003e gromacs.mdrun(v=True, deffnm=\"md\")\n\n\n\t \nLicense\n=======\n\nThe **GromacsWrapper** package is made available under the terms of\nthe `GNU Public License v3`_ (or any higher version at your choice)\nexcept as noted below. See the file COPYING for the licensing terms\nfor all modules.\n\n.. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html\n\n\nInstallation\n============\n\nReleases\n--------\n\nThe `latest version of GromacsWrapper from PyPi`_ can be installed\nwith ::\n\n  pip install GromacsWrapper\n\n\nor as a `conda-forge package`_ with ``conda`` from the *conda-forge* channel ::\n\n   conda install -c conda-forge gromacswrapper\n    \n\n.. _`latest version of GromacsWrapper from PyPi`:\n   https://pypi.org/project/GromacsWrapper/\n\n.. _`conda-forge package`:\n   https://anaconda.org/conda-forge/gromacswrapper\n\n\nDevelopment version\n-------------------\n\nThe *main* branch in the GitHub source repository generally\ncontains useful code but nevertheless, things can break in weird and\nwonderful ways. Please report issues through the `Issue Tracker`_.\n\nTo use the *development code base*:  checkout the ``main`` branch::\n\n   git clone https://github.com/Becksteinlab/GromacsWrapper.git   \n\nand install ::\n\n   pip install GromacsWrapper/\n\nCode contributions are welcome. We use `black`_ for uniform code\nformatting so please install black_ and run it on your code.\n\n.. _`black`: https://github.com/psf/black\n\nDownload and Availability\n=========================\n\nThe GromacsWrapper home page is\nhttp://github.com/Becksteinlab/GromacsWrapper.  The latest release of the\npackage is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases\n\nYou can also clone the `GromacsWrapper git repository`_ or fork for\nyour own development::\n\n  git clone git://github.com/Becksteinlab/GromacsWrapper.git\n\nQuestions\n=========\n\nPlease ask questions in the `Discussion forum`_ (instead of private email).\n\n\nReporting Bugs and Contributing to GromacsWrapper\n=================================================\n\nPlease use the `Issue Tracker`_ to report bugs, installation problems,\nand feature requests. Ask questions in the `Discussion forum`_.\n\n**Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a \ngeneral introduction on how make a pull request and contribute to open source projects.\n\n.. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues\n.. _Discussion forum: https://github.com/Becksteinlab/GromacsWrapper/discussions\n\n\nBuilding Documentation\n======================\n\nInstall Sphinx::\n\n   pip install sphinx\n\nand compile::\n\n  cd GromacsWrapper\n  python setup.py build_sphinx\n  \n\nCiting\n======\n\n|zenodo|\n\nGromacsWrapper was written by Oliver Beckstein with contributions from\nmany other people. Please see the file AUTHORS_ for all the names.\n\nIf you find this package useful and use it in published work I'd be\ngrateful if it was acknowledged in text as\n\n  \"... used GromacsWrapper (Oliver Beckstein et al,\n  https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)\"\n\nor in the Acknowledgements section.\n\nThank you.\n\n.. _AUTHORS:\n   https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/main/AUTHORS\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fgromacswrapper","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbecksteinlab%2Fgromacswrapper","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbecksteinlab%2Fgromacswrapper/lists"}