msm_we

Code for Markov state modeling of weighted ensemble trajectories.

• Authors: John Russo, Jeremy Copperman
• Free software: MIT license
• Documentation: https://jdrusso.github.io/msm_we/ .

Features

• Compute a history-augmented Markov state model from WESTPA weighted ensemble data
• Estimate steady-state distributions
• Estimate flux profiles
• Estimate committors

Known Issues

• Sometimes, on Python3.7 (and maybe below) the subprocess calls will fail. This may manifest as a silent failure,

followed by hanging (which is very fun to debug!) To fix this, upgrade to Python 3.8+.

Code development TODOs

• Provide option for user to override dimReduce() in case they want to do something other than PCA/VAMP
• Add TICA option to dimReduce()

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.