molPX and TICA with BPTI

• molPX intro
  • Input types and typical usecase
  • Visualize a FES and the molecular structures behind it
  • Visualize trajectories, FES and molecular structures
    • Again, we have commented out some parameters that provide more control on the output of visualize.traj. Uncomment them and see what happens
• Intermediate steps: using molpx to generate a regspace sample of the data
  • Link the PDF plot with the sampled structures and visually explore the FES
• Paths samples along the different projections (=axis)
  • Link the PDF plot with the sampled paths/structures and visually explore the coordinates (separately).
• Interaction with PyEMMA
  • Use a clustering object as input
  • Visual representations for MSMs
  • TPT Reactive Pathway Representation