|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:
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/
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
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