MolSSI Coding Workshop


Assistant Professor of Physics and Biology, Cal State LA


Assistant Professor of Chemistry, UC Davis


Professor of Chemistry, Iowa State University


Molecular Sciences Software Institute (MolSSI) is pleased to announce a workshop for MERCURY attendees to learn beginning programming skills. This two-session coding workshop will be held on the afternoon of Saturday, July 22 and morning of Sunday, July 23, 2017 and be open to up to 30 attendants. During the workshop you will learn some basics of running and analyzing molecular dynamics simulations using OpenMM and MDTraj, how to use GitHub as a repository for software, how to make modifications to these software packages, and how to submit those changes for inclusion in the GitHub repository. Paul Nerenberg (California State University, Los Angeles), Lee-Ping Wang (University of California, Davis), and Theresa Windus (Iowa State University) will lead you through hands-on exercises and simulations. Each student is expected to bring their own laptop and to complete an interactive, free Python tutorial before the workshop. Specific reading, software download (+ installation) instructions, and instructional materials will be provided after registration. The tentative schedule is listed below.

Saturday, July 22

  • 1:30-3:45 pm   Review of basic Python concepts; intro to MD with OpenMM
  • 3:45-4:15 pm   Coffee/Snack break
  • 4:15-5:45 pm   Intro to MD (cont.); basic MD trajectory analysis and visualization with MDTraj

Sunday, July 23

  • 8:45-9:45 am             Git and GitHub
  • 9:45-10:15 am           Coffee/snack break
  • 10:15 am-12:00 pm   Putting it together: making a new feature in OpenMM, logging the changes with Git, and pushing them to GitHub
  • 12:00 pm-1:30 pm      Lunch