index.txt

.. MDpow documentation master file, created by
   sphinx-quickstart on Wed Mar 24 13:28:55 2010.

.. Common replacements for MDPOW docs
..
.. |Pow| replace:: *P*\ :sub:`OW`
.. |P_OW| replace:: *P*\ :sub:`OW`
.. |POW|  replace:: *P*\ :sub:`OW`
.. |P_ow| replace:: *P*\ :sub:`OW`
.. |P_cw| replace:: *P*\ :sub:`CW`

MDPOW documentation
===================

*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 coeffcients. Currently implemented:

- *water-octanol* partition coefficient (|P_ow|)
- *water-cyclohexane* partition coefficient (|P_cw|)

Calculations are performed with the Gromacs_ MD software
package [#GromacsWrapper]_. Currently, *OPLS-AA force field* 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.icsn.cnrs-gif.fr/
.. _ParamChem: https://cgenff.paramchem.org/

.. rubric:: Contents:

.. toctree::
   :maxdepth: 2

   INSTALL
   init
   scripts
   equil
   fep
   analysis
   utilities      
   tables

.. rubric:: Footnotes

.. [#GromacsWrapper] The package is built on top of the `GromacsWrapper`_
                     framework (which is automatically installed).


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`