===================
README for MDPOW
===================
|build| |cov| |docs| |black| |zenodo|
.. |P_ow| replace:: *P*\ :sub:`OW`
.. |P_cw| replace:: *P*\ :sub:`CW`
.. |P_tw| replace:: *P*\ :sub:`TW`
*MDPOW* is a python package that automates the calculation of
solvation free energies via molecular dynamics (MD) simulations. In
particular, it facilitates the computation of partition
coefficients. Currently implemented:
- *water-octanol* partition coefficient (|P_ow|)
- *water-cyclohexane* partition coefficient (|P_cw|)
- *water-toluene* partition coefficient (|P_tw|)
Calculations are performed with the Gromacs_ MD software package
[#GromacsWrapperNote]_. Currently, *OPLS-AA*, *CHARMM/CGENFF*, and
*AMBER/GAFF* parameters are supported.
As *input*, the user only needs to provide a structure file (PDB or
GRO) and a Gromacs ITP file containing the parametrization of the
small molecule (e.g. from LigandBook_ or ParamChem_).
.. _Gromacs: http://www.gromacs.org
.. _GromacsWrapper: http://gromacswrapper.readthedocs.org/en/latest/
.. _LigandBook: http://ligandbook.org/
.. _ParamChem: https://cgenff.paramchem.org/
Documentation
-------------
* https://mdpow.readthedocs.io
* `Tutorial`_ : computing the octanol-water partition coefficient of
benzene (uses the `example files`_)
.. _Tutorial: http://mdpow.readthedocs.io/en/latest/init.html#tutorial-using-the-mdpow-scripts-to-compute-logpow-of-benzene
.. _example files: https://github.com/Becksteinlab/MDPOW/tree/develop/doc/examples
Installation
------------
See `INSTALL`_ for detailed instructions. MDPOW currently supports and
is tested with Python 3.10 to 3.12.
You will also need `Gromacs`_ (currently tested with versions 4.6.5,
2018, 2020, 2021, 2022, 2023, 2024 but 2016 and 2019 should also work).
Development version
~~~~~~~~~~~~~~~~~~~
If you want to install the development version, get the sources from
GitHub (the development branch) ::
git clone https://github.com/Becksteinlab/MDPOW.git
and Install from the checked out source::
pip install MDPOW/
(Note the trailing slash ``/`` to indicate the directory.)
Source code
-----------
*MDPOW* is open source and published under the `GNU General Public License
v3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .
We use `black`_ for uniform code formatting.
.. _`GNU General Public License v3`:
http://www.gnu.org/licenses/gpl-3.0.html
.. _`black`: https://github.com/psf/black
Footnotes
---------
.. [#GromacsWrapperNote] The package is built on top of the GromacsWrapper_
framework (which is automatically installed).
.. |build| image:: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml/badge.svg?branch=develop
:alt: Build Status
:target: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml
.. |cov| image:: https://codecov.io/github/Becksteinlab/MDPOW/coverage.svg?branch=develop
:alt: Coverage Status
:target: https://codecov.io/github/Becksteinlab/MDPOW?branch=develop
.. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest
:target: http://mdpow.readthedocs.org/en/latest/?badge=latest
:alt: Documentation
.. |zenodo| image:: https://zenodo.org/badge/44999898.svg
:target: https://zenodo.org/badge/latestdoi/44999898
:alt: Zenodo
.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
:alt: black
.. _INSTALL: INSTALL.rst
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"description": "===================\n README for MDPOW\n===================\n\n|build| |cov| |docs| |black| |zenodo|\n\n.. |P_ow| replace:: *P*\\ :sub:`OW`\n.. |P_cw| replace:: *P*\\ :sub:`CW`\n.. |P_tw| replace:: *P*\\ :sub:`TW` \n\n*MDPOW* is a python package that automates the calculation of\nsolvation free energies via molecular dynamics (MD) simulations. In\nparticular, it facilitates the computation of partition\ncoefficients. Currently implemented:\n\n- *water-octanol* partition coefficient (|P_ow|)\n- *water-cyclohexane* partition coefficient (|P_cw|)\n- *water-toluene* partition coefficient (|P_tw|)\n \nCalculations are performed with the Gromacs_ MD software package\n[#GromacsWrapperNote]_. Currently, *OPLS-AA*, *CHARMM/CGENFF*, and\n*AMBER/GAFF* parameters are supported.\n\nAs *input*, the user only needs to provide a structure file (PDB or\nGRO) and a Gromacs ITP file containing the parametrization of the\nsmall molecule (e.g. from LigandBook_ or ParamChem_).\n\n.. _Gromacs: http://www.gromacs.org\n.. _GromacsWrapper: http://gromacswrapper.readthedocs.org/en/latest/\n.. _LigandBook: http://ligandbook.org/\n.. _ParamChem: https://cgenff.paramchem.org/\n\n\nDocumentation\n-------------\n\n* https://mdpow.readthedocs.io\n* `Tutorial`_ : computing the octanol-water partition coefficient of\n benzene (uses the `example files`_)\n\n\n.. _Tutorial: http://mdpow.readthedocs.io/en/latest/init.html#tutorial-using-the-mdpow-scripts-to-compute-logpow-of-benzene\n.. _example files: https://github.com/Becksteinlab/MDPOW/tree/develop/doc/examples\n\nInstallation\n------------\n\nSee `INSTALL`_ for detailed instructions. MDPOW currently supports and\nis tested with Python 3.10 to 3.12.\n\nYou will also need `Gromacs`_ (currently tested with versions 4.6.5,\n2018, 2020, 2021, 2022, 2023, 2024 but 2016 and 2019 should also work).\n\n\nDevelopment version\n~~~~~~~~~~~~~~~~~~~\n\nIf you want to install the development version, get the sources from\nGitHub (the development branch) ::\n\n git clone https://github.com/Becksteinlab/MDPOW.git\n\nand Install from the checked out source::\n\n pip install MDPOW/\n\n(Note the trailing slash ``/`` to indicate the directory.)\n\n\n\nSource code\n-----------\n\n*MDPOW* is open source and published under the `GNU General Public License\nv3`_. Source code is available at https://github.com/Becksteinlab/MDPOW .\n\nWe use `black`_ for uniform code formatting.\n\n.. _`GNU General Public License v3`:\n http://www.gnu.org/licenses/gpl-3.0.html\n\n.. _`black`: https://github.com/psf/black\n\n\nFootnotes\n---------\n\n.. [#GromacsWrapperNote] The package is built on top of the GromacsWrapper_\n framework (which is automatically installed).\n\n.. |build| image:: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml/badge.svg?branch=develop\n :alt: Build Status\n :target: https://github.com/Becksteinlab/MDPOW/actions/workflows/ci.yaml\n\n.. |cov| image:: https://codecov.io/github/Becksteinlab/MDPOW/coverage.svg?branch=develop\n :alt: Coverage Status\n :target: https://codecov.io/github/Becksteinlab/MDPOW?branch=develop\n\n.. |docs| image:: https://readthedocs.org/projects/mdpow/badge/?version=latest\n :target: http://mdpow.readthedocs.org/en/latest/?badge=latest\n :alt: Documentation\n \n.. |zenodo| image:: https://zenodo.org/badge/44999898.svg\n :target: https://zenodo.org/badge/latestdoi/44999898\n :alt: Zenodo\n\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.. _INSTALL: INSTALL.rst\n",
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