MolSSI School on Open Source Software for Rare-Event Sampling Strategies: POSTPONED TO 2022

Organized by Prof. Lillian Chong (U. of Pittsburgh) and Daniel Zuckerman (Oregon Health & Science U.), this two-day school will present both lectures and tutorials on open-source software for simulating rare events (e.g., protein folding, protein binding, chemical reactions) and related tasks. The school will feature a variety of topics and packages that are contributing to modern, rigorous enhanced sampling of non-equilibrium processes in biomolecules.

The goals of the school are:

  • To explain and demonstrate the latest developments in path sampling platforms and associated software.
  • To tackle common challenges (g. identification of relevant progress coordinates) in development of various rare-event sampling strategies.
  • To determine how to improve the interoperability between the packages.

Confirmed speakers and tentative titles:

  • Peter Bolhuis – “Efficient Generation and Analysis of Rare-Event Trajectory Ensembles with OpenPathSampling”
  • John Chodera – “Unifying transition path sampling, weighted ensemble methods, and adaptive Markov state model construction and reconstruction of unbiased dynamics”
  • Lillian Chong – “WESTPA: Advances in weighted ensemble software and hybrid QM/MM applications”
  • Alex Dickson – “High-dimensional weighted ensemble algorithms: Rates, free energies, and mechanisms for extremely rare events”
  • Alan Grossfield – “Analyzing molecular dynamics simulations with LOOS”
  • Sapna Sarupia – “Forward Flux methods: the good, the bad, the ugly”
  • Rebecca Wade – “Computing ligand-protein residence times using tauRAMD”
  • Daniel Zuckerman – “Learning from history to get rates and mechanism from trajectories”


(i) WESTPA software for executing the weighted ensemble strategy,

(ii) OPS software for applying transition path sampling strategies,

(iii) RAMD machine learning approach for estimating relative ligand residence times,

(iv) LOOS and PyEmma software packages for simulation analysis, and

(v) BioSimSpace software for facilitating the use of various molecular dynamics engines.

The school is targeted to graduate students doing research in molecular simulations, as well as postdoctoral fellows and faculty at undergraduate institutions interested in learning about rare-event sampling strategies.  Participants must be familiar with carrying out standard molecular dynamics simulations with their preferred dynamics engine (OpenMM, NAMD, Amber, etc.). In addition, in order to “hit the ground running” during the two-day school, participants should have completed introductory tutorials of the WESTPA and OPS software packages before attending the school. Social events and discussions to foster collaboration are planned. Registration is free. Single-occupancy dorm rooms at the University of Pittsburgh will be available at no cost. Any funds remaining after the completion of the school will be used to help defray travel costs for student participants. The application deadline will be updated once new dates have been identified.  Visit THIS LINK for the application form.