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. See our docs.
Installation
The easiest way to install the pymbar
release is via conda:
conda install c omnia 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 have the nsamples
sampled oscillator positions x_n
(with samples from all states concatenated), reduced potentials in the (nstates,nsamples)
matrix u_kn
, number of samples per state in the nsamples
array N_k
, and indices s_n
denoting which thermodynamic state each sample was drawn from.
To analyze this data, we first initialize the MBAR
object:
>>> mbar = MBAR(u_kn, N_k)
Estimating dimensionless free energy differences between the sampled thermodynamic states and their associated uncertainties (standard errors) simply requires a call to getFreeEnergyDifferences()
:
>>> results = mbar.getFreeEnergyDifferences(return_dict=True)
Here results
is a dictionary with keys Deltaf_ij
, dDeltaf
, and Theta
. Deltaf_ij[i,j]
is the matrix of dimensionless free energy differences f_j  f_i
, dDeltaf_ij[i,j]
is the matrix of standard errors in this matrices estimate, and Theta
is a covariance matrix that can be used to propagate error into quantities derived from the free energies.
By default, return_dict
is False
and the return will be a tuple.
Expectations and associated uncertainties can easily be estimated for observables A(x)
for all states:
>>> A_kn = x_kn # use position of harmonic oscillator as observable
>>> results = mbar.computeExpectations(A_kn, return_dict=True)
where results
is a dictionary with keys mu
, sigma
, and Theta
, where mu[i]
is the array of the estimate for the average of the observable for in state i, sigma[i]
is the estimated standard deviation of the mu
estimates, and Theta[i,j]
is the covarinace matrix of the log weights.
See the docstring help for these individual methods for more information on exact usage; in Python or IPython, you can view the docstrings with help()
.
Authors
 Kyle A. Beauchamp kyle.beauchamp@choderalab.org
 John D. Chodera john.chodera@choderalab.org
 Levi N. Naden levi.naden@choderalab.org
 Michael R. Shirts michael.shirts@virginia.edu
References

Please cite the original MBAR paper:
Shirts MR and Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. J. Chem. Phys. 129:124105 (2008). DOI

Some timeseries algorithms can be found in the following reference:
Chodera JD, Swope WC, Pitera JW, Seok C, and Dill KA. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J. Chem. Theor. Comput. 3(1):2641 (2007). DOI

The automatic equilibration detection method provided in
pymbar.timeseries.detectEquilibration()
is described here:Chodera JD. A simple method for automated equilibration detection in molecular simulations. J. Chem. Theor. Comput. 12:1799, 2016. DOI
License
pymbar
is free software and is licensed under the MIT license.
Thanks
We would especially like to thank a large number of people for helping us identify issues
and ways to improve pymbar
, including Tommy Knotts, David Mobley, Himanshu Paliwal,
Zhiqiang Tan, Patrick Varilly, Todd Gingrich, Aaron Keys, Anna Schneider, Adrian Roitberg,
Nick Schafer, Thomas Speck, Troy van Voorhis, Gupreet Singh, Jason Wagoner, Gabriel Rocklin,
Yannick Spill, Ilya Chorny, Greg Bowman, Vincent Voelz, Peter Kasson, Dave Caplan, Sam Moors,
Carl Rogers, Josua Adelman, Javier Palacios, David Chandler, Andrew Jewett, Stefano Martiniani, and Antonia Mey.
Notes

alchemicalanalysis.py
described in this publication has been relocated here.