Flexible Length TPS on Alanine Dipeptide

This example shows how to set up, run, and analyze a 2-state TPS simulation. The system studied is alanine dipeptide, which Peter Bolhuis likes to say is “the hydrogen atom of biomolecules” – it has enough complexity to illustrate the ideas of biomolecular simulation, but is small enough that even when solvated, a full TPS simulation can run on a laptop and be converged overnight.

This example consists of three notebooks: one to create an initial trajectory from a high-temperature run, one to run TPS, and one to analyze the TPS results. These notebooks can be found in the OpenPathSampling GitHub repository.

• Obtaining an equilibrated initial trajectory
  • Setting up high-temperature engine
  • Defining states
  • Getting a first trajectory
  • Plotting the trajectory
  • Setting up the normal temperature engine
  • Using TPS to equilibrate
• Running the production TPS simulation
  • Load simulation objects from file
  • Run TPS
• Analyzing the flexible path length simulation
  • Replica history tree and decorrelated trajectories
  • Path length distribution
  • Path density histogram
  • Convert to MDTraj for analysis by external tools