Amber masthead
Filler image AmberTools20 Amber20 Manuals Tutorials Force Fields Contacts History
Filler image

Useful links:

Amber Home
Download Amber
Installation
News
Amber Citations
GPU Support
Intel Support
Updates
Mailing Lists
For Educators
File Formats

10.6 Jupyter Notebooks and Python

10.6.1 An Introduction to PYTRAJ

This tutorial will give a basic introduction to using PYTRAJ for performing trajectory analysis in Jupyter notebook.

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.

By Hai Nguyen

10.6.3 Using Jupyter notebook remotely

This tutorial will guide you how to use Jupyter notebook remotely.

By Hai Nguyen

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.

By Hai Nguyen

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.

By Hai Nguyen

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.

By Hai Nguyen

"How's that for maxed out?"

Last modified: Sep 23, 2020