Useful links:

Jupyter Notebooks and Python

An Introduction to PYTRAJ
This tutorial will give a basic introduction to using PYTRAJ for performing trajectory analysis in Jupyter notebook. By Hai Nguyen.

Simulating Crystals with AMBER Molecular Dynamics - Jupyter notebook version
This tutorial combines Jupyter notebok, PYTRAJ and protein viewer and other packages in AMBER for seting up system for crystal simulation. By Hai Nguyen.

Using Jupyter notebook remotely
This tutorial will guide you how to use Jupyter notebook remotely. By Hai Nguyen.

Using NGLView for protein visualization in Jupyter notebook
This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to use pytraj to perform data analysis. By Hai Nguyen.

Trajectory rendering and movie making with NGLView
This tutorial will guide you how to use NGLView to visualize MD trajectories in Jupyter notebook and to quickly make a movie for presentation. By Hai Nguyen.

Real time molecular dynamics simulation and visualization
This tutorial will guide you how to use AmberTools and NGLView to perform molecular dynamics simulation and visualize the trajectory in real time. By Hai Nguyen.