Learn to Code in GROMACS Online Workshop

The 2024 edition of the workshop “Learn to code in GROMACS” ( www.gromacs.org/workshop.html ) was held over three days from the 10th to the 12th of September. The workshop brought together forty-four attendees and ten mentors from different countries, both from academia and industry, for this online event. Forty-four people attended the online lectures, while only a restricted number of attendees (eleven) were selected for the hands-on session to guarantee an optimal ratio between attendees and mentors (one-to-one).

On the first day, Sebastian Wingbermuehle ( www.biophysics.se/index.php/members/sebastian-wingbermuhle ) introduced “GROMACS GitLab and version control”, and, in the afternoon, Mark Abraham ( www.linkedin.com/in/mark-abraham-5a329599 ) spoke about “Software structure and interface”. The following day, Andrey Alekseenko ( www.biophysics.se/index.php/members/andrey-alekseenko ) gave a presentation on “Testing and testing infrastructure”, and, on the last days, Berk Hess ( www.biophysics.se/index.php/members/berk-hess ) spoke about “Everything around coding”, giving a historical overview of GROMACS developments. The event closed with a roundtable discussion featuring a panel with Andrey Alekseenko, Berk Hess, Mark Abraham and Magnus Lundborg ( www.biophysics.se/index.php/members/magnus-lundborg ).

Mentoring took place online via breakout rooms. There were a total of eleven mentors who were from Sweden, Germany, France and the USA. During the hands-on session, the attendees each worked closed together with a mentor to address a pre-selected GROMACS issue. The issues were labelled as “2024 workshop” in the GROMACS GitLab repository ( gitlab.com/gromacs/gromacs ). The scope was such that the attendees could participate in and directly experience the whole review process. At the end of the workshop, five out of over fourteen selected issues had been closed. To avoid attendees getting stuck on a problem, they were asked to report the status of the issue they worked on at the beginning of each section. According to the type of problem, one or more mentors met with the attendee in the breakout room. We observed that assigning a reference mentor to each issue encouraged the attendees to ask questions. The lectures were recorded and posted on the BioExcel YouTube channel: Learn to Code in GROMACS ( www.youtube.com/playlist?list=PLzLqYW5ci-2d82Pbcv9r712NQlCgjF-2E ) and were uploaded on Zenodo Workshop: Learn to code in GROMACS (2024) ( zenodo.org/records/13739992 ). We hope that the collected material will be re-used in the future to build self-learning tutorials.

The organisers would like to extend a big “thank you” to Andrey, Berk, Magnus, Mark and all the other mentors: Amr Alhossary ( gitlab.com/aalhossary ), Eliane Briand ( gitlab.com/ElianeBriand ), Giacomo Fiorin ( research.ninds.nih.gov/staff-directory/giacomo-fiorin-phd ), Hubert Santuz ( gitlab.com/HubLot ), Lukas Müllender ( gitlab.com/lmuellender ), Michele Pellegrino ( gitlab.com/michele.pellegrino ), and Vedran Miletic ( vedran.miletic.net ).

If you are interested in attending the next edition of the “Learn to Code in GROMACS” workshop, keep an eye on bioexcel.eu/events  for announcements.

Above: Learn to code in GROMACS online workshop, 10-12 September 2024