MolSSI Workshops

Molecular Sciences Software Institute (MolSSI) is pleased to announce a workshop for MERCURY attendees to learn skills relevant for computational molecular science research. This two-day workshop will be held July 18 and 19, 2023 and be open to up to 40 attendees. During the workshop you have the opportunity to write programs and work in a collaborative software development environment. The MM Tools workshop introduces students to fundamental concepts in molecular mechanics and molecular dynamics, including setting up a force field file and running a simulation with OpenMM. Prior experience with Python programming is assumed, equivalent to the MolSSI Python Scripting workshop. The workshop will allow flexibility for different levels of molecular dynamics simulation experience, so both students with no prior experience in molecular dynamics as well as students with some experience are encouraged to register.

Aurelia Ball (Skidmore College), Kedan He (Eastern Connecticut State University), and Frank Vazquez (St. John’s University) will lead you through hands-on exercises and calculations. Each student is expected to bring their own laptop running a recent version of Windows or macOS and be familiar with basic Python (e.g., lessons 1-6 of MolSSI Python Scripting for Computational Molecular Science). Specific instructions regarding software downloads and installation will be provided after registration. The tentative schedule is listed below. All sessions are in Patrick Lecture Hall – Room 126 / Plyler Hall (Tentative).

Tuesday, July 18

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

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

3:30-4:45 pm: Activity – Trajectory analysis of alkane simulations

6:00-7:30 pm: DINNER

Wednesday, July 19

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

11:15 am-12:15 pm: Git and GitHub

12:15-1:30 pm: LUNCH

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