Useful links:
10.6.1 An Introduction to PYTRAJ
This tutorial will give a basic introduction to using PYTRAJ for performing trajectory analysis in Jupyter notebook.
PYTRAJ
By Hai Nguyen
10.6.2 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.
10.6.3 Using Jupyter notebook remotely
This tutorial will guide you how to use Jupyter notebook remotely.
10.6.4 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.
10.6.5 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.
10.6.6 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.
NGLView
"How's that for maxed out?"
Last modified: Mar 5, 2023
