MolSSI Coding Workshop @ MERCURY 2018

The MolSSI will host a coding workshop at the upcoming 2018 MERCURY Consortium conference at Furman University, July 18-19.  This workshop will offer up to 50 undergraduate attendees at the conference an opportunity to learn the fundamentals 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 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.

You may register for the workshop and MERCURY conference here.

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