2021 MolSSI School on Open Source Software in Rare Event Path Sampling Strategies

Tutorials and Other Learning Materials

Below are video lectures/tutorials that have been prepared for your interests. Please revisit us here after the completion of the 2021 Virtual MolSSI School for additional resources.

• Introduction to Weighted Ensemble Simulation by Daniel Zuckerman and Getting ready for WESTPA 2.0 by Anthony Bogetti. See also WESTPA wiki.
• Wepy tutorial for simulating ligand dissociation by Alex Dickson.
• Open Path Sampling (OPS) tutorial by David Swenson. See also GitHub repo.
• Tau-RAMD tutorial: Fast estimation of drug residence times by Daria Kokh & Rebecca Wade
• LOOS MD analysis tutorial by Alan Grossfield: YouTube and slides
• Tutorials for using the BioSimSpace interoperability layer for different MD engines offered by CCP-BioSim

Lecture Videos from the MolSSI School

Day 1 (June 8)

• Lillian Chong (University of Pittsburgh)
  • WESTPA: Advances in weighted ensemble software and recent applications
• Alan Grossfield (University of Rochester)
  • Analyzing molecular dynamics simulations with LOOS
• Greg Bowman (Washington University in St. Louis)
  • Goal-oriented adaptive sampling and potential synergies with weighted ensembles
• Rebecca Wade (Heidelberg Institute for Theoretical Studies)
  • Session was not recorded due to the interactive nature.
  • Computing ligand-protein residence times using tauRAMD (Recording of a previous talk)

Day 2 (June 15)

• Peter Bolhuis (University of Amsterdam)
  • Efficient Generation and Analysis of Rare-Event Trajectory Ensembles with OpenPathSampling
• Alex Dickson (Michigan State University)
  • High-dimensional weighted ensemble algorithms: Rates, free energies, and mechanisms for extremely rare events
• Sapna Sarupia (Clemson University)
  • Forward Flux methods: the good, the bad, the ugly
• Daniel Zuckerman (Oregon Health & Science University)
  • Learning from history to get rates and mechanism from trajectories