-
Notifications
You must be signed in to change notification settings - Fork 54
Tutorials
To become acquainted with the WE/WESTPA, we recommend reading the introduction to the weighted ensemble strategy and working through the suite of WESTPA tutorials in LiveCoMS, which features the use of WESTPA with the AMBER and OpenMM dynamics engines; all files you will need for WESTPA 2.0 are here. Additional tutorials for WESTPA with the NAMD dynamics engine is also available. For guidance on the use of WESTPA with the GROMACS dynamics engines, check out our older tutorials, which we are updating for WESTPA 2.0 and the latest versions of GROMACS.
Also included in the LiveCOMS article are six other Advanced Tutorials (7.5-7.10) which highlight new features and methods we've added to WESTPA 2.0. A prerequisite for these tutorials is completion of the Basic and Intermediate Tutorials (7.1-7.4). All files can be found in the Tutorials repository.
We strongly suggest that you complete the checklist each time you set up a WESTPA simulation. Also listed below are WESTPA protocols for selected showcase applications, additional tutorials, and videos of relevant presentations from previous WESTPA workshops are provided below.
Introduction to Weighted Ensemble
WESTPA Tutorials LiveCOMS Paper
WESTPA protocols for showcase applications not covered in our LiveCoMS tutorials can be found in the publications below. When available, links to scripts are also provided.
- Protein-peptide binding in implicit solvent (coupled folding and binding of a disordered peptide). [pdf]
- Protein-protein binding in explicit solvent. [pdf] [scripts]
- Millisecond to seconds timescale protein folding in implicit solvent. [pdf]
- Microsecond protein folding in explicit solvent. [pdf]
Variations of the basic_nacl tutorial can be found in the westpa_tutorials repository. These include variations for using Amber with WESTPA, running WESTPA on GPUs (with GPU optimized MD code) and an example of using the ZMQ work manager with WESTPA, which is useful for running on multiple nodes at once. Tutorials for using WESTPA with NAMD is also included in the same additional_tutorials folder.
The following tutorials are archived and no longer maintained and designed for WESTPA 1.0 (v2020.XX). However, they can be useful if one is interested in certain special cases of using WESTPA and/or further details about the setup of simulations after completing the LiveCoMS tutorials.
- Na+/Cl- Association with AMBER 16
- Na+/Cl- Association with GROMACS 2021.2
- Na+/Cl- Association with NAMD 2.12
- Na+/Cl- Association with OpenMM 5.1
- WCA Dimer with OpenMM 7.4
- Protein Folding (Chignolin) with AMBER 16
- Protein Folding (Chignolin) with NAMD
- Old Quickstart Guide
- Old LiveCoMS tutorial files for WESTPA 1.0