WESTPA 1.0¶
Overview¶
WESTPA is a package for constructing and running stochastic simulations using the “weighted ensemble” approach of Huber and Kim (1996) (see overview).
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).
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 GNU General Public
License, Version 3. See the file COPYING
for more information.
Obtaining and Installing WESTPA¶
Here are the simple instructions for installing WESTPA as a package within Anaconda or Miniconda.
1. Begin by installing the most recent Python 2.7.x version of either Anaconda or Miniconda.
2. Open a command line terminal and type the following command.
conda install -c conda-forge westpa
3. Prior to running simulations or performing analysis, execute the following commands or add the commands to your ~/.bashrc file.
export ENV_PREFIX="$(dirname $(dirname `which python2.7`))"
. $ENV_PREFIX/westpa-2017.10/westpa.sh
4. To use WESTPA after the installation, execute the following command in a terminal. This will "power on" the WESTPA environment.
conda activate westpa-2017.10
After performing your WESTPA simulations, you can execute the following command in a terminal to "power down" the WESTPA environment.
conda deactivate
For other types of installations, including setting up WESTPA inside a virtual environment, installing from the tar.gz file and detailed instructions on how to obtain Anaconda or Miniconda, please visit our full installation page here.
Getting help¶
FAQ¶
Responses to frequently asked questions (FAQ) can be found in the following page:
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.
Further, all WESTPA command-line tools (located in westpa/bin
) 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.
Copyright, license, and warranty information¶
For WESTPA¶
The WESTPA package is copyright (c) 2013, Matthew C. Zwier and Lillian T. Chong. (Individual contributions noted in each source file.)
WESTPA is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
WESTPA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program (see the included file COPYING
). If not,
see <http://www.gnu.org/licenses/>.
Unless otherwise noted, source files included in this distribution and lacking a more specific attribution are subject to the above copyright, terms, and conditions.
For included software¶
Distributions of WESTPA include a number of components without modification, each of which is subject to its own individual terms and conditions. Please see each package’s documentation for the most up-to-date possible information on authorship and licensing. Such packages include:
- h5py
- See lib/h5py/docs/source/licenses.rst
- blessings
- See lib/blessings/LICENSE
In addition, the wwmgr
work manager is derived from the concurrent.futures
module (as included in Python 3.2) by Brian Quinlan and
copyright 2011 the Python Software Foundation. See http://docs.python.org/3/license.html for more information.