Molecular Mechanics Tools

The mm-tools workshop introduces molecular dynamics simulations using the software OpenMM, and analysis of simulation results using MDTraj. The theoretical background of MD simulations are discussed, and students simulate and analyze alkane and a simple protein system. This workshop also covers putting code on GitHub and includes an exercise where students implement a new software feature and submit a pull request.


Students should be familiar with opening the Terminal window and creating and navigating files in bash. They should have basic familiarity with python scripting, equivalent to what would be learned in the MolSSI Python Data and Scripting workshop.


Setup Download files required for the lesson
00:00 1. Introduction What does molecular mechanics mean?
What is a force field?
How do I tell software what my force field is?
01:00 2. MD Simulation of Alkanes How do I run a simulation?
How do I analyze a simulation?
03:00 3. MD Simulation of a Protein How do I run a simulation for a protein?
How do I analyze a simulation for a protein?
04:30 4. Git and GitHub How do I share code and collaborate on code with others using git and GitHub?
05:30 5. Putting It All Together How do I implement a new feature in someone else’s code and then share my new feature?
06:50 Finish

The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.