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.