The registration to this course will open in January. 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 (AH)
15.00h – Setup and Analysis Hands On (AH)
16.00h – Break
16.30h – Setup and Analysis Hands On (AH)  
18.00h – Adjourn

Day 2

Session 3
09.00h – Simulation DBs (MoDEL) (PA)
10.00h – Simulation Data Management (PA)
10.30h – Break
11.00h – Coarse Grained MD (PD)
12.00h – Application Examples (PD)
13.00h – Break

Session 4
14.00h – Nucleic acids and chromatin Coarse-Grained simulation (JW)
16.00h – Break
16.30h – Free Hands-on
18.00h – End of the course

PD: Pablo Dans (IRB-Barcelona)

JW: Jurgen Walther (IRB-Barcelona)

https://events.prace-ri.eu/event/655/