Great introductory slides on MD and WE by Prof. Matthew Zwier!


WE Review Paper: Zuckerman, Daniel M., and Lillian T. Chong. "Weighted ensemble simulation: review of methodology, applications, and software." Annual review of biophysics 46 (2017): 43.

WESTPA 2.0: Russo, John D., et al. "WESTPA 2.0: High-performance upgrades for weighted ensemble simulations and analysis of longer-timescale applications." Journal of Chemical Theory and Computation 18.2 (2022): 638-649.

WESTPA 1.0 (older version but still has a valuable overview of the WESTPA program): Bogetti, Anthony T., et al. "A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0]." Living journal of computational molecular science 1.2 (2019).

GaMD: Miao, Yinglong, Victoria A. Feher, and J. Andrew McCammon. "Gaussian accelerated molecular dynamics: unconstrained enhanced sampling and free energy calculation." Journal of chemical theory and computation 11.8 (2015): 3584-3595.

  • Additional reading and websites to get started on the weighted ensemble (WE) method:

An example of how WE is able to sample biologically relevant timescales

Download the latest WESTPA here for your workstation and supercomputer cluster

Installation for PowerPC architecture, etc. (alternative installations) can be found here

Checklist for WESTPA simulation

Using the HDF5 trajectory storage scheme

Minimal adaptive binning scheme video

WESTPA tutorials

Q&A forum for WESTPA

How west.h5 is structured

Getting thermodynamic and kinetic properties from WESTPA simulations