This workshop was designed to go over the basics of molecular dynamics (MD) simulations with OpenMM, and using MDAnalysis for trajectory analysis.
Prerequisites
Students should be familiar with using the Terminal to execute commands, as well as creating and editing text files. The workshop was designed to start from lesson 3. Lessons 1-2, as well as the extra episodes, contain additional background information for students that are unfamiliar with biomolecular simulation and/or Python.
| Setup | Download files required for the lesson | |
| 00:00 | 1. Python Basics |
What are Python packages?
What are comments and docstrings? How do I use variables? What are if statements, for loops, and counters? How do I write a function in Python? |
| 01:00 | 2. Structure Preparation |
How do I make a structure biologically relevant?
Do I need to add hydrogens? Where do parameters come from? How do I add ions and solvate a system? |
| 03:00 | 3. OpenMM |
How do I set up an OpenMM molecular dynamics simulation in Python?
What information can OpenMM provide as the simulation is running? |
| 03:30 | 4. MDAnalysis |
How are structure and trajectory files read with Python?
What is an atom group? How do I apply analyses to residues, instead of individual atoms? How can tabular data files and plots be generated with Python? |
| 04:00 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.