https://github.com/becksteinlab/mdpow
Calculation of water/solvent partition coefficients with Gromacs.
https://github.com/becksteinlab/mdpow
free-energy gromacs gromacswrapper molecular-dynamics python science
Last synced: about 1 month ago
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Calculation of water/solvent partition coefficients with Gromacs.
- Host: GitHub
- URL: https://github.com/becksteinlab/mdpow
- Owner: Becksteinlab
- License: gpl-3.0
- Created: 2015-10-26T21:58:15.000Z (over 9 years ago)
- Default Branch: develop
- Last Pushed: 2024-10-14T20:03:58.000Z (7 months ago)
- Last Synced: 2025-04-09T20:08:04.937Z (about 1 month ago)
- Topics: free-energy, gromacs, gromacswrapper, molecular-dynamics, python, science
- Language: Python
- Homepage: https://mdpow.readthedocs.io
- Size: 739 MB
- Stars: 26
- Watchers: 4
- Forks: 9
- Open Issues: 32
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGES
- License: COPYING
- Authors: AUTHORS
Awesome Lists containing this project
README
===================
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