NCC and CoE Collaboration: BioExcel Workshop on GROMACS and HADDOCK
On October 18 and 19, 2023, a workshop focused on working with GROMACS and HADDOCK software tools was held in Bratislava. The workshop was the result of cooperation between competence centers in Slovakia, v Austria, Czech Republic and Hungary with BioExcel center of excellence. The BioExcel CoE team develops both applications, so experienced lecturers could not only show common simulations and modeling, but also answer specific questions from participants.
The workshop was held in a hybrid format. As the host organization was NCC Slovakia (with the support of the Austrian NCC), the new Slovak supercomputer Devana was used for hands-on exercises. In addition to the theoretical lecture, during the first day, the participants tried molecular dynamics simulation for a simple membrane protein using GROMACS, including setting up the input files, as well as the simulation itself for energy minimization and data production. The exercise was carried out using an interactive Jupyter notebook. An interesting part was the calculations with the use and comparison of the performance of the application on CPU and GPU computing servers.
The second day of the workshop was devoted to the HADDOCK tool, which is used for integrative modeling of various types of biomolecular systems and their interactions. The HADDOCK3 version is currently available, which offers a modular workflow setup in addition to data-driven docking. The user can choose his own combination of independent modules for his specific case.
Links to the materials can be found on the workshop page HEREWe would like to thank all partners and we believe that the lectures and workshops were beneficial for the participants. We also believe that we will be able to offer similar events in the future thanks to our cooperation with the EuroCC community and centers of excellence.
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