Notebooks

Course notebooks

The notebooks are rendered as local HTML (in the rendered folder) and can also be downloaded as .ipynb.

• Episode 1: Introduction (simple)
• Episode 1: Introduction (complex)
• Episode 2: Running simulations (simple)
• Episode 2: Running simulations (complex)
• Episode 3: Preparing and editing the system (simple)
• Episode 3: Preparing and editing the system (complex)
• Episode 4: Advanced sampling (simple)
• Episode 4: Advanced sampling (complex)
• Episode 4: Advanced sampling (REMD)
• Episode 4: Advanced sampling (GaMD)
• Episode 4: Advanced sampling (Martini)
• Episode 5: Analysis (simple)
• Episode 5: Analysis (complex)
• Episode 6: PyEMMA (pentapeptide)
• Episode 7: deeptime (Ala2 example)

If you prefer to download the notebooks:

• Download notebooks