A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0]

Area of Science:

• Computational Chemistry
• Biophysics
• Systems Biology

Background:

• The Weighted Ensemble (WE) strategy is effective for rare event simulations in molecular dynamics.
• WESTPA software facilitates WE simulations for processes like protein folding and binding.

Purpose of the Study:

• To provide comprehensive tutorials for WESTPA software, covering basic and advanced Weighted Ensemble simulations.
• To guide users on best practices for preparing, executing, and analyzing WE simulations for diverse applications.

Main Methods:

• Two sets of tutorials are presented: basic and advanced.
• Basic tutorials cover molecular association, host-guest binding, peptide sampling, and protein folding.
• Advanced tutorials focus on WESTPA 2.0 features like binless schemes, adaptive binning, HDF5 data handling, rate estimation, Python API, and specialized plugins.

Main Results:

• The tutorials demonstrate applications for atomistic and non-spatial models, including protein folding and membrane permeability.
• Users will learn to apply WE simulations to complex processes and large datasets.
• Best practices for efficient simulation and analysis are detailed.

Conclusions:

• These tutorials enhance the usability of the WESTPA software for advanced rare event simulations.
• The WESTPA 2.0 features enable more efficient simulation and analysis of complex biological and chemical processes.
• The provided resources cater to users with prior experience in molecular dynamics or systems biology simulations.