Registration for this event is open
Our third Ambassador Program workshop is jointly organised and supported by our colleagues at the National Competence Centres in Bulgaria, Romania, Serbia and North Macedonia. The hands-on workshop is aimed at Ph.D. students and post-docs and will be a hybrid (on-site/online) event focusing on the use of the following BioExcel core codes: GROMACS, HADDOCK and PMX.
Date: 21 – 22 May 2025
Venue: Sofia, Bulgaria
Participation: Open application with a selection. 30 applicants will be selected for on-site participation and 10 on-line. Applicants from Bulgaria, Montenegro, North Macedonia, Romania and Serbia will be prioritised for on-site participation. We can only accept participants from EuroHPC Joint Undertaking member institutions.
Registration fee: none
Registration deadline: 15 April 2025
Registration process: as part of the registration you will need to submit your CV, a motivation letter and a brief outline of your research interests. Further information regarding this can be found via the registration link above.
Program:
Day 1 – Wednesday 21 May 2025
| Time (EEST) | Topic |
| 09:00 – 09:45 | Registration |
| 09:45 – 10:00 | Opening |
| 10:00 – 11:00 | Lecture: Integrative modelling with HADDOCK |
| 11:00 – 11:30 | Break |
| 11:30 – 13:30 | Practical: HADDOCK tutorial on antibody-antigen modelling |
| 13:30 – 14:30 | Lunch |
Trainers: Alexandre Bonvin, Vlad Cojocaru
| Time (EEST) | Topic |
| 14:30 – 15:30 | Lecture: Molecular Dynamics using GROMACS |
| 15:30 – 16:00 | Break |
| 16:00 – 17:30 | Practical: Tutorial on introduction to Molecular Dynamics simulations |
| 17:30 – 18:00 | Break |
| 18:00 – 19:00 | Practical: Enhanced sampling with AWH |
| 19:00 – 20:00 | Free |
| 20:00 – 22:30 | Social dinner |
Trainers: Alessandra Villa, Catherine Bergh
Day 2 – Thursday 22 May 2025
| Time (EEST) | Topic |
| 10:00 – 11:00 | Lecture: Alchemical free energy calculations with PMX/GROMACS |
| 11:00 – 11:30 | Break |
| 11:30 – 13:00 | Practical: Tutorial on amino acid mutations with PMX |
| 13:00 – 14:00 | Lunch |
Trainers: Bert de Groot
| Time (EEST) | Topic |
| 14:00 – 15:00 | Lecture: Efficient use of CPU resources in GROMACS simulations |
| 15:00 – 15:30 | Break |
| 15:30 – 17:00 | Practical: Efficient use of CPU resources in GROMACS simulations |
| 17:00 – 17:30 | Closing remarks |
Trainers: Andrey Alekseenko
