.. -*- mode: rst, coding: utf-8 -*-
.. The whole GromacsWrapper package is Copyright (c) 2009-2018 Oliver
.. Beckstein and AUTHORS except where noted otherwise.
========================
README: GromacsWrapper
========================
|build| |cov| |docs| |zenodo| |black| |PRsWelcome| |anaconda|
A primitive Python wrapper around the Gromacs_ tools. The library is
tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, 2021.x, 2022.x,
2023.x (and 5.x and 2016.x should also work). It supports Python 2.7
and 3.6--3.11 on Linux and macOS.
GromacsWrapper also provides a small library (cook book) of often-used
recipes and helper functions to set up MD simulations.
`Documentation`_ is mostly provided through the python doc strings and
available at https://gromacswrapper.readthedocs.org for recent releases.
The source code is available in the `GromacsWrapper git repository`_.
Please be aware that this is **beta** software that most definitely
contains bugs. It is *your* responsibility to ensure that you are
running simulations with sensible parameters.
.. _Gromacs: http://www.gromacs.org
.. _Documentation:
https://gromacswrapper.readthedocs.org/en/latest/
.. _GromacsWrapper git repository:
https://github.com/Becksteinlab/GromacsWrapper
.. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=main
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:target: https://codecov.io/gh/Becksteinlab/GromacsWrapper
:alt: Code Coverage
:scale: 100%
.. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg
:target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper
:alt: Latest release on zenodo (with DOI)
.. |docs| image:: https://readthedocs.org/projects/gromacswrapper/badge/?version=latest
:target: https://gromacswrapper.readthedocs.org/en/latest/?badge=latest
:alt: Documentation
.. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
:target: http://makeapullrequest.com
:alt: PRs Welcome!
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:target: https://anaconda.org/conda-forge/gromacswrapper
:alt: Anaconda.org package
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
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Quick Start
===========
Given a PDB file ``1iee.pdb``, set up and run a simple simulation (assuming
you have all other input files at hand such as the MDP files)::
>>> import gromacs
>>> print(gromacs.release)
2018.2
>>> help(gromacs.pdb2gmx)
DESCRIPTION
gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,
adds hydrogens to the molecules and generates coordinates in GROMACS
...
...
OPTIONS
Options to specify input files:
-f [<.gro/.g96/...>] (eiwit.pdb)
Structure file: gro g96 pdb brk ent esp tpr
...
...
>>> gromacs.pdb2gmx(f="1iee.pdb", o="protein.gro", p="topol.top",
... ff="oplsaa", water="tip4p")
>>> gromacs.editconf(f="protein.gro", o="boxed.gro",
... bt="dodecahedron", d=1.5, princ=True,
... input="Protein")
>>> gromacs.solvate(cp="boxed.gro", cs="tip4p", p="topol.top",
... o="solvated.gro")
>>> gromacs.grompp(f="emin.mdp", c="solvated.gro", p="topol.top",
... o="emin.tpr")
>>> gromacs.mdrun(v=True, deffnm="emin")
>>> gromacs.grompp(f="md.mdp", c="emin.gro", p="topol.top", o="md.tpr")
>>> gromacs.mdrun(v=True, deffnm="md")
License
=======
The **GromacsWrapper** package is made available under the terms of
the `GNU Public License v3`_ (or any higher version at your choice)
except as noted below. See the file COPYING for the licensing terms
for all modules.
.. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html
Installation
============
Releases
--------
The `latest version of GromacsWrapper from PyPi`_ can be installed
with ::
pip install GromacsWrapper
or as a `conda-forge package`_ with ``conda`` from the *conda-forge* channel ::
conda install -c conda-forge gromacswrapper
.. _`latest version of GromacsWrapper from PyPi`:
https://pypi.org/project/GromacsWrapper/
.. _`conda-forge package`:
https://anaconda.org/conda-forge/gromacswrapper
Development version
-------------------
The *main* branch in the GitHub source repository generally
contains useful code but nevertheless, things can break in weird and
wonderful ways. Please report issues through the `Issue Tracker`_.
To use the *development code base*: checkout the ``main`` branch::
git clone https://github.com/Becksteinlab/GromacsWrapper.git
and install ::
pip install GromacsWrapper/
Code contributions are welcome. We use `black`_ for uniform code
formatting so please install black_ and run it on your code.
.. _`black`: https://github.com/psf/black
Download and Availability
=========================
The GromacsWrapper home page is
http://github.com/Becksteinlab/GromacsWrapper. The latest release of the
package is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases
You can also clone the `GromacsWrapper git repository`_ or fork for
your own development::
git clone git://github.com/Becksteinlab/GromacsWrapper.git
Questions
=========
Please ask questions in the `Issue Tracker`_ (instead of private email).
Reporting Bugs and Contributing to GromacsWrapper
=================================================
Please use the `Issue Tracker`_ to report bugs, installation problems,
and feature requests. Ask questions in the `Discussion forum`_.
**Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a
general introduction on how make a pull request and contribute to open source projects.
.. _Issue Tracker: https://github.com/Becksteinlab/GromacsWrapper/issues
.. _Discussion forum: https://github.com/Becksteinlab/GromacsWrapper/discussions
Building Documentation
======================
Install Sphinx::
pip install sphinx
and compile::
cd GromacsWrapper
python setup.py build_sphinx
Citing
======
|zenodo|
GromacsWrapper was written by Oliver Beckstein with contributions from
many other people. Please see the file AUTHORS_ for all the names.
If you find this package useful and use it in published work I'd be
grateful if it was acknowledged in text as
"... used GromacsWrapper (Oliver Beckstein et al,
https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"
or in the Acknowledgements section.
Thank you.
.. _AUTHORS:
https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/main/AUTHORS
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"description": ".. -*- 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 (and 5.x and 2016.x should also work). 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It is *your* responsibility to ensure that you are\nrunning 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/badge.svg\n :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper\n :alt: Code Coverage\n :scale: 100%\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 >>> import gromacs\n >>> print(gromacs.release)\n 2018.2\n >>> 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 [<.gro/.g96/...>] (eiwit.pdb)\n Structure file: gro g96 pdb brk ent esp tpr\n ...\n ...\n >>> gromacs.pdb2gmx(f=\"1iee.pdb\", o=\"protein.gro\", p=\"topol.top\",\n ... ff=\"oplsaa\", water=\"tip4p\")\n >>> gromacs.editconf(f=\"protein.gro\", o=\"boxed.gro\",\n ... bt=\"dodecahedron\", d=1.5, princ=True,\n ... input=\"Protein\")\n >>> gromacs.solvate(cp=\"boxed.gro\", cs=\"tip4p\", p=\"topol.top\",\n ... o=\"solvated.gro\")\n >>> gromacs.grompp(f=\"emin.mdp\", c=\"solvated.gro\", p=\"topol.top\",\n ... o=\"emin.tpr\")\n >>> gromacs.mdrun(v=True, deffnm=\"emin\")\n >>> gromacs.grompp(f=\"md.mdp\", c=\"emin.gro\", p=\"topol.top\", o=\"md.tpr\")\n >>> 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 `Issue Tracker`_ (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. 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