Python implementation of the multistate Bennett acceptance ratio
pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimating expectations and free energy differences from equilibrium samples from multiple probability densities.
Installation
The easiest way to install the pymbar release is via conda:
conda install -c conda-forge pymbar
You can also install pymbar from the Python package index using pip:
pip install pymbar
The development version can be installed directly from github via pip:
pip install git+https://github.com/choderalab/pymbar.git
Usage
Basic usage involves importing pymbar and constructing an MBAR object from the reduced potential of simulation or experimental data.
Suppose we sample a 1D harmonic oscillator from a few thermodynamic states:
>>> from pymbar import testsystems
>>> [x_n, u_kn, N_k, s_n] = testsystems.HarmonicOscillatorsTestCase().sample()
We