Obtaining the code

If you have Mercurial installed, you can clone the repository using:

$ hg clone

Alternatively, you can download a compressed archive of the code by going to and selecting the Branches tab and selecting one of the archive formats for the default branch.


This code makes use of a number of freely available third-party libraries. You must first install WESTPA ( and all of its dependencies. This package also makes use of several additional libraries for analyzing data generated by the simulations:

It is generally recommended to use either the Enthought Python Distribution (Academic) or the Anaconda distribution (CE or Pro) to install all of the basic dependencies. Then install bottleneck and pymbar either into that version of python or into a separate directory that is on the PYTHONPATH. The code assumes that the dependencies are available through the python executable returned by which python, and that you are using a bash based shell on a Unix system (both Linux and OS X should work).


A Makefile is provided to build all of the python extension included in the package and setup the run scripts, environmental variables and symbolic links. First set $WEST_ROOT to the directory containing the WESTPA package:

$ export WEST_ROOT=<path to WEST-PA install>

and then run make:

$ cd stringmethodexamples
$ make

The Weighted Ensemble-based string method provides an efficient algorithm for sampling equilibrium and non-equilibrium transitions in complex systems.

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