Online course: GROMACS for ARCHER2 users

We have used effort from EuroCC (the UK’s National Competence Centre in HPC, HPDA and AI, which we lead in collaboration with STFC Hartree) to increase the hands-on support we can offer to course attendees. Such support is especially important for online courses. 

A course which we have recently delivered is “Introduction to GROMACS”. GROMACS is a free molecular dynamics package primarily used for bio-molecular simulations of proteins, lipids and nucleic acids. Widely used for research, it is one of the most popular molecular dynamics codes, and one of the most used pieces of software on ARCHER2. 

The Introduction to GROMACS course was aimed at ARCHER2 users who are either new to using GROMACS or are new to using it in an HPC environment. These users are sometimes referred to as “package users”, that is they are using a software package developed for HPC use, and as a user they don’t have to know parallel programming but do need to know how to best use HPC resources. With the support of EuroCC this course was run with additional hands-on support. 

As with most courses run since the pandemic it was delivered in an online, live format. The platform used was Blackboard Collaborate – a virtual classroom with screensharing, chat, and breakout room functionality.  

The course material was presented using a Software Carpentries-style format, where presenter and attendees work through the same web page which contains both the background information and the hands-on practical exercises. Additionally a live document  enables attendees and the instructor to share code, commands, output, and results. While the lead instructor takes the course, multiple helpers monitor the chat to answer specific questions or offer additional help to ensure people are not left behind. Throughout such courses, multiple polls are conducted to check where attendees have got to, and the course timescales are adjusted as required to cater to the needs of the audience. 

Our GROMACS course began by explaining how to log into ARCHER2 and use basic HPC commands. It then described how to set up a biomolecular system – the example used was a small protein (PDB ID 5PEP) shown in the image below.  

A more theoretical overview of molecular simulation was given once attendees were comfortable logging into ARCHER2 and using basic GROMACS commands. This was followed by how to run the simulations on the ARCHER2 compute nodes. Next, visualisation and analysis techniques were covered. Finally, the course discussed guidance on how to get the best computational performance and the attendees completed a longer exercise benchmarking the program with different parallel settings.  

Material from the course is available at https://www.archer2.ac.uk/training/courses/220421-intro-gromacs/. 

Courses delivered by EPCC

See our website for other training delivered by EPCC: Training courses at EPCC.