resources
Great introductory slides on MD and WE by Prof. Matthew Zwier!
MUCCC22-SternerZwier.pdfSeminal papers for Ahn lab members:
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
Getting thermodynamic and kinetic properties from WESTPA simulations