The registration to this course is closed. 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
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Day 2
Session 3
09.00h – Simulation DBs (MoDEL) (RG)
10.00h – Simulation Data Management (PA)
10.30h – Break
11.00h – Coarse Grained MD (AE)
12.00h – Application Examples (MO)
13.00h – Break
Session 4
14.00h – Coarse Grained MD manual slides Hands on (AE)
16.00h – Break
16.30h – Free Hands-on
18.00h – End of the course
AE: Agustí Emperador (IRB) , AH: Adam Hospital (IRB), JLG: Josep Ll. Gelpi (BSC-IRB- UB), MO: Modesto Orozco (BSC-IRB-UB), PA: Pau Andrio (BSC), RG: Ramón Goñi (BSC)
