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 (POW)
- water-cyclohexane partition coefficient (PCW)
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).
Contents:
- Quick installation instructions for POW
mdpow
— Computing the octanol/water partitioning coefficient- The
mdpow-*
scripts mdpow.equil
— Setting up and running equilibrium MDmdpow.fep
– Calculate free energy of solvationmdpow.analysis
— Collection of analysis and plotting functions- Helper modules
- Tables of hard-coded values used in mdpow
Footnotes
[1] | The package is built on top of the `GromacsWrapper`_ framework (which is automatically installed). |