A Suite of Tutorials for the WESTPA Rare-Events Sampling Software [Article v1.0]

Area of Science:

• Biophysics
• Computational Chemistry
• Molecular Dynamics

Background:

• The weighted ensemble (WE) strategy is efficient for simulating rare events like protein folding and binding.
• Atomistic molecular dynamics (MD) simulations are crucial for understanding molecular mechanisms.
• WESTPA is a software package designed for WE simulations.

Purpose of the Study:

• To provide comprehensive tutorials on applying the WE strategy using WESTPA.
• To guide users in best practices for preparing, executing, and analyzing WE simulations.
• To cover diverse applications including molecular association, host-guest binding, peptide dynamics, and protein folding.

Main Methods:

• Development and presentation of five distinct tutorials for WESTPA.
• Demonstration of WE simulations for various biomolecular processes.
• Integration with common MD engines (Amber, Gromacs, OpenMM).

Main Results:

• Users will gain practical skills in setting up and running WE simulations.
• Tutorials cover a range of complexities from simple association to complex folding.
• Best practices for analysis of WE simulation data are provided.

Conclusions:

• The WE strategy, implemented in WESTPA, offers an efficient approach for rare event simulations.
• These tutorials serve as a valuable resource for researchers utilizing WE for biomolecular studies.
• Proficiency in standard MD simulations is a prerequisite for utilizing these advanced WE tutorials.