westpa 2022.7

Overview

WESTPA is a package for constructing and running stochastic simulations using the “weighted ensemble” approach of Huber and Kim (1996). For use of WESTPA please cite the following:

Zwier, M.C., Adelman, J.L., Kaus, J.W., Pratt, A.J., Wong, K.F., Rego, N.B., Suarez, E., Lettieri, S., Wang, D.W., Grabe, M., Zuckerman, D.M., and Chong, L.T. “WESTPA: An Interoperable, Highly Scalable Software Package For Weighted Ensemble Simulation and Analysis,” J. Chem. Theory Comput., 11: 800−809 (2015).

Russo, J. D., Zhang, S., Leung, J.M.G., Bogetti, A.T., Thompson, J.P., DeGrave, A.J., Torrillo, P.A., Pratt, A.J., Wong, K.F., Xia, J., Copperman, J., Adelman, J.L., Zwier, M.C., LeBard, D.N., Zuckerman, D.M., Chong, L.T. WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications. J. Chem. Theory Comput., 18 (2): 638–649 (2022).

See this page and this powerpoint for an overview of weighted ensemble simulation.

To help us fund development and improve WESTPA please fill out a one-minute survey and consider contributing documentation or code to the WESTPA community.

WESTPA is free software, licensed under the terms of the MIT License. See the file LICENSE for more information.

Requirements

WESTPA is written in Python and requires version 3.7 or later. WESTPA also requires a number of Python scientific software packages. The simplest way to meet these requirements is to download the Anaconda Python distribution from www.anaconda.com (free for all users).

WESTPA currently runs on Unix-like operating systems, including Linux and Mac OS X. It is developed and tested on x86_64 machines running Linux.

Obtaining and Installing WESTPA

WESTPA is developed and tested on Unix-like operating systems, including Linux and Mac OS X.

Regardless of the chosen method of installation, before installing WESTPA, we recommend you to first install the Python 3 version provided by the latest free Anaconda Python distribution. After installing Anaconda, create a new python environment for the WESTPA install with the following:

conda create -n westpa-2.0 python=3.9
conda activate westpa-2.0

Then, we recommend installing WESTPA through conda or pip. Execute either of the following:

conda install -c conda-forge westpa

or:

python -m pip install westpa

See the install instructions on our wiki for more detailed information.

To install from source (not recommended), start by downloading the corresponding tar.gz file from the releases page. After downloading the file, unpack the file and install WESTPA by executing the following:

tar xvzf westpa-main.tar.gz
cd westpa
python -m pip install -e .

Getting started

High-level tutorials of how to use the WESTPA software can be found here. Further, all WESTPA command-line tools provide detailed help when given the -h/–help option.

Finally, while WESTPA is a powerful tool that enables expert simulators to access much longer timescales than is practical with standard simulations, there can be a steep learning curve to figuring out how to effectively run the simulations on your computing resource of choice. For serious users who have completed the online tutorials and are ready for production simulations of their system, we invite you to contact Lillian Chong (ltchong AT pitt DOT edu) about spending a few days with her lab and/or setting up video conferencing sessions to help you get your simulations off the ground.

Getting help

WESTPA FAQ

A mailing list for WESTPA is available, at which one can ask questions (or see if a question one has was previously addressed). This is the preferred means for obtaining help and support. See http://groups.google.com/group/westpa-users to sign up or search archived messages.

Developers

Search archived messages or post to the westpa-devel Google group: https://groups.google.com/group/westpa-devel.