MolSSI Coding Workshop

Aurelia Ball

Assistant Professor of Chemistry, Skidmore College

Paul Nerenberg

Assistant Professor of Physics and Biology, Cal State LA

Theresa Windus

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 July 18 and 19, 2018 and be open to up to 50 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), Aurelia Ball (Skidmore College), 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.

Wednesday, July 18


Session I

  • 9:30-10 AM: Installation help for those who need it
  • 10-10:15 AM: Intro and welcome
  • 10:15-11 AM: Lecture – Intro to molecular mechanics/force fields
  • 11:00 AM-12:00 PM: Activity – Create a force field file 
  • 12:00-1:30 PM: LUNCH

Session II

  • 1:30-2:00 PM: Getting familiar with Anaconda environment and using Jupyter notebooks
  • 2:00-2:15 PM: Lecture – Intro to molecular dynamics
  • 2:15-3:00 PM: Activity – MD simulations of alkanes
  • 3:00-3:30 PM: SNACK BREAK

Session III

  • 3:30-4:45 PM: Activity – Trajectory analysis of alkane simulations 
  • 6:00-7:30 PM: DINNER

Thursday, July 19

Session IV

  • 9:00-9:30 AM: Activity – MD simulation of BPTI
  • 9:30-9:45 AM: Lecture – Brief primer on protein dihedral angles
  • 9:45-10:45 AM: Activity – Trajectory analysis of BPTI simulation
  • 10:45-11:15 AM: SNACK BREAK

Session V

  • 11:15 AM-12:15 PM: Git and GitHub
  • 12:15-1:30 PM: LUNCH

Session VI

  • 1:30-3:30 PM: Putting it together: making a new feature in OpenMM, logging the changes with Git, and pushing them to GitHub