This lesson provides an introduction to using GROMACS. GROMACS is a free molecular dynamics package primarily used for simulating biochemical molecules like proteins, lipids, and nucleic acids. The program is widely used, and a large number of publications based on work simulated using GROMACS is published every year.

For this lesson, attendees will learn how to prepare, run, and analyse GROMACS simulations on the ARCHER2 high-performance computing facility. Attendees will learn:

• How to login to ARCHER2, load modules, and run jobs.
• How to use GROMACS functions to generate a fully-solvated, charge-neutral GROMACS structure file from a protein database file.
• How to prepare and run a GROMACS simulation of this structure file.
• How to analyse and visualise GROMACS simulations once they’ve run.
• How to determine whether your GROMACS simulations are running optimally.

Target Audience:

This introductory course is intended for anyone interested in learning the basics of GROMACS and how to use it. Course attendees will be expected to know how to use the command line and how to SSH into a remote computer system.