Description
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. Attendess will learn:
- How to login to ARCHER2, load modules, and run jobs.
- How to use GROMACS functions to take generate a fully-solvated, charge-neutral GROMACS structure file from a protein databas 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.
This introductory course is intended for anyone interested in learning the basics of GROMACS and how to use it.
General Information
Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). They are also required to abide by the ARCHER2 Training Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
- The room is wheelchair / scooter accessible.
- Accessible restrooms are available.
Materials will be provided in advance of the lesson and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.
Contact: Please email H.Judge@epcced.ac.uk for more information.
Prerequisites
You should have used remote HPC facilities before. In particular, you should be happy with connecting using SSH, know what a batch scheduling system is and be familiar with using the Linux command line. You should also be happy editing plain text files in a remote terminal (or, alternatively, editing them on your local system and copying them to the remote HPC system using
scp). Finally, you should be comfortable with compiling parallel HPC source code that uses MPI and OpenMP.