| Start date: | 18 Oct 2023, 09:00 (CEST) | Entry level: | Basic / Intermediate | |
| End date: | 19 Oct 2023, 14:00 (CEST) | Subject area: | Computational biomolecular research | |
| Location: | Bratislava, Slovakia & ONLINE | Topics: | GROMACS, HADDOCK | |
| Language: | English | Target audience: | Academia, industry, public sector | |
| Price: | Free (for eligible participants) | Organizers: | EuroCC SK, AT, CZ, HU & BioExcel-CoE |
The National Competence Centres for HPC in Slovakia, Austria, Czechia and Hungary, together with BioExcel – Centre of Excellence in HPC – are organizing a 1,5-day workshop focused on the GROMACS software package. The focus will be on the basic usage and deployment on GPU-accelerated HPC systems, the agenda will also cover more of the core modules for GROMACS developed by BioExcel (HADDOCK).
The workshop will take place in Bratislava, which can be reached conveniently from all involved countries: Slovakia, Czechia, Austria and Hungary. Participants from the rest of the EuroCC network are welcome, too! The event is organized in hybrid format, however, in-person participation is strongly encouraged. Attending in-person will allow you to get the most of the workshop, to interact closely with the lecturers during the lectures and practical exercises – simply to learn more!
Agenda & Content
Day 1, 18 October 2023, GROMACS:
09:00-09:05 Welcome
09:05-09:10 BioExcel Introduction
09:10-09:45 Introduction to molecular dynamics simulation and GROMACS (part I)
09:45-10:00 Q&A
10:00-10:30 Introduction to molecular dynamics simulation and GROMACS (part II)
10:30-10:45 Q&A
10:45-11:15 Break
11:15-12:45 Tutorial GROMACS: Protein Membrane
12:45-14:00 Lunch
14:00-14:30 Running GROMACS on CPU and GPU
14:30-14:45 Q&A
14:45-15:15 Hands-on
15:15-15:45 Break
15:45-16:30 Hands-on
18:00-22:00 Social dinner
Day 2, 19 October 2023, HADDOCK:
09:00 - 10:30 Integrative modelling with HADDOCK
10:30-11:00 Break
11:00-12:45 Tutorial - HADDOCK
12:45-14:00 Lunch
Please see the main BioExcel workshop on GROMACS and HADDOCK page for all further details and updates.
Target audience
Course for academia, industry, and public administration.
Course format
The event is organized in HYBRID format, however, in-person participation (in Bratislava) is recommended for a better learning experience.
Hands-on labs
You will need your own laptop to be able to participate in the hands-on parts. HPC system Devana will be used for the workshop. Access information and instructions will be provided shortly before the workshop.
Lecturers
Lecturers from BioExcel – the leading European Centre of Excellence for Computational Biomolecular Research – will deliver the training.
Day 1, 18 October 2023, GROMACS: Alessandra Villa, Catherine Bergh, and Farzaneh Jalalypour
Day 2, 19 October 2023, HADDOCK: Rodrigo Vargas, Alexander Bonvin, and Marco Giulini
Language
English
Date, time, and location
18.10.2023 (09:00 – 16:30 CEST) & 19.10.2023 (09:00 – 14:00 CEST),
Faculty of Natural Sciences, Comenius University Bratislava, room CPS+ (room number is B1-322)
Faculty address: Mlynská dolina, Ilkovičova 6, 842 15 Bratislava, GPS : 48°09’00,12″ | 17°04’17,85″
& ONLINE (Hybrid format)
Please see the main BioExcel workshop on GROMACS and HADDOCK page for all further details and updates.
In-person participation is strongly encouraged. Attending in-person will allow you to get the most of the workshop, to interact closely with the lecturers during the lectures and practical exercises – simply to learn more!
Prices and eligibility
Access to the workshop venue and programme is free of charge for registered participants. Light meals and coffee breaks will be provided by the local organizers.
Registration
Registration for this training event is handled by NCC Slovakia through the main BioExcel workshop on GROMACS and HADDOCK page.
Registration for this event is closed.
All further details
Please see the main BioExcel workshop on GROMACS and HADDOCK page for all further details (directions, travel, accommodation).
Organizers
This training event is jointly organized by the NCCs Slovakia, Austria, Czechia, and Hungary – the National Competence Centres for HPC together with BioExcel – the leading European Centre of Excellence for Computational Biomolecular Research.
Acknowledgements
This course is partially funded by the EuroCC 2 project.
The project has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 101101903. The JU receives support from the Digital Europe Programme and Austria, Belgium, Bulgaria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Luxembourg, Montenegro, Netherlands, North Macedonia, Norway, Poland, Portugal, Romania, Serbia, Slovakia, Slovenia, Spain, Sweden, and Türkiye.
Additional funding for the project comes from the Austrian federal ministries BMBWF and BMK.
