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
- Running the production TPS simulation
- Analyzing the flexible path length simulation