Mar 14 – 15, 2018
Barcelona BSC Campus Nord
CET timezone

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)



Barcelona BSC Campus Nord
Vertex Building, Room S208

For further details and practical info such as local transport and venue please visit the local course pages for PATC@BSC: