The registration to this course is now open. Please, bring your own laptop. All the PATC courses at BSC are free of charge.
Objectives: The course will make the attendants familiar with simulation technologies used in Life Sciences and their specific adaptation to HPC environment
Course convener: Josep Gelpi
Detailed outline:
Introduction to biomolecular simulation
Coarse-grained and atomistic simulation strategies
Automated setup for simulation
HPC specifics: Large scale parallelization, use of GPU’s
Storage and strategies for large scale trajectory analysis
Learning Outcomes: Setup, execute, and analyze standard simulations in HPC environment
Level: (All courses are designed for specialists with at least 1st cycle degree or similar background experience) INTERMEDIATE: for trainees with some theoretical and practical knowledge.
Course Program Outline:
Day 1 Session 1 09.00h – Welcome & Introduction (JLG) 10.30h – Break 11.00h – Atomistic MD Algorithm (JLG) 11.45h – Algorithm improvements & HPC (JLG) 12.30h – Break Session 2 14.00h – Simulation Setup (FB) 15.30h – Break 16.30h – Setup and Analysis Hands On (PA) 18.00h – Adjourn -------------------------------------------------------------------------------------------------------- Day 2 Session 3 09.00h – Simulation DBs and Data Management (PA) 10.30h – Break 11.00h – Coarse Grained MD (PD) 12.00h – Application Examples (PD) 13.00h – Break Session 4 14.00h – Trajectory visualization and analysis (PA) 16.00h – Break 16.30h – Report writing (FB, PA) 18.00h – End of the course PD: Pablo Dans (IRB-Barcelona) PA: Pau Andrio (BSC) FB: Federica Battistini (IRB-Barcelona)
