Multiple State TIS on a Toy Model

This example covers the use the multiple state TIS on a simple toy model. We recommend new users start by working through these notebooks because (1) these notebooks have the most detailed discussion, and (2) the systems are simple enough that the simulations can be run interactively.

This example consists of three notebooks: one to obtain initial trajectories, one to perform the TIS simulation, and one to do the analysis after.

For more advanced techniques based on the same system, see the subsequent notebooks in the directory containing these examples.

• Obtaining the first trajectories for a Toy Model
  • Basic system setup
    • Set up the toy system
    • Set up the engine
    • Defining states and interfaces
    • Build the MSTIS transition network
  • Bootstrap to fill all interfaces
  • Storing stuff
• Running an MSTIS simulation
  • Setting up the simulation
    • Loading from storage
    • Creating new interface set, network, and move scheme
  • Preparing initial conditions
  • Equilibration
  • Production
  • Appendix: Alternate equilibration scheme
• Analyzing the MSTIS simulation
  • Reaction rates
    • Total crossing probability
    • Flux
    • Conditional transition probability
  • Path ensemble properties
    • Interface crossing probabilities
    • Path length histograms
  • Sampling properties
    • Move scheme analysis
    • Replica exchange sampling
      • Replica exchange mixing matrix
      • Replica exchange graph
      • Replica exchange flow
    • Replica move history tree
    • Visualizing trajectories
  • Histogramming data (TODO)