10-13 April 2017
Stockholm, Sweden
Europe/Stockholm timezone

Scientific Programme

PRACE, in collaboration with BioExcel Center of Excellence, are bringing together for the first time the main developers of four of the major and most popular codes for molecular modelling and simulations - GROMACS, AMBER, NAMD and VMD. This is a great opportunity for novice and experienced users to learn from the very authors of the software.

The 2017 Spring School program will allow participants to get a comprehensive introduction to the different codes; to understand their scalability and performance, as well as ways to avoid potential issues;  to learn the best practices about using them on HPC systems. Extensive hands-on sessions will cover more than half of time during the school.

The course will take place at the computer laboratories of PDC Center for High Performance Computing at KTH Royal Institute of Technology in Stockholm. Participants will be able to run on the PRACE Tier­‐1 system Beskow, the largest Tier-1 system within the Nordic countries.

The school is also supported by the Swedish National Infrastructure for Computing (SNIC).

Programme

Time

  Topic Trainer Location
Day 1 – Monday 10th April 2017
08:30-09:00  Registration   E3
09:00-09:15 Welcome  Michaela Barth  E3
09:15-10:00  BioExcel Center of Excellence – Training Programme  Vera Matser E3
10:00-10:30  Coffee break    
10:30-12:00  Molecular visualisations with VMD  John Stone E3
12:00-13:00  Lunch    
13:00-13:45  Introduction to PDC supercomputing environment Henric Zazzi E3
 13:45-15:00  Hands-on VMD   Red / Orange
 15:00-15:30  Coffee break    
 15:30-17:30  Hands-on VMD   Red / Orange
 17:30  Welcome Dinner   Syster o Bror
Day 2 – Tuesday 11th April 2017
 09:30 – 10:30  HPC Simulations with NAMD  Jim Phillips E3
 10:30 – 11:00  Group picture and coffee Break   Campus
11:00 – 12:00  HPC Simulations with NAMD   E3
12:00 – 13:00  Lunch    
13:00 – 14:30  Hands-on NAMD   Red / Orange
14:30 – 15:00  Coffee Break    
15:00 – 17:00  Hands-on NAMD   Red / Orange
Day 3 – Wednesday 12th April 2017
 09:30 – 10:30  HPC Simulations with GROMACS  Erik Lindahl E3
 10:30 – 11:00  Coffee Break    
11:00 – 12:00  HPC Simulations with GROMACS   E3
12:00 – 13:00  Lunch    
13:00 – 14:30  Hands-on GROMACS   Red / Orange
14:30 – 15:00  Coffee Break    
15:00 – 17:00  Hands-on GROMACS   Red / Orange
18:00  Guided Tour and Dinner   Vasa Museum
Day 4 – 13th April 2017
 09:30 – 10:30  HPC Simulations with AMBER  Tom Cheatham E3
 10:30 – 11:00  Coffee Break    
 11:00 – 12:00  HPC Simulations with AMBER   E3
 12:00 – 13:00  Lunch    
 13:00 – 14:30  Hands-on AMBER   Red / Orange
 14:30 – 15:00  Coffee Break    
 15:00 – 15:15  Course Feedback Vera Matser Red / Orange
 15:15 – 17:00  Hands-on AMBER   Red / Orange

 

 

After the course completion, the participants will be able to:

  •     create computer models of typical simulation systems such as solvated and membrane embeded proteins;
  •     run large parallel simulations on HPC machines;
  •     learn advanced topics on efficient usage of special accelerators such as GPUs;
  •     visualize and analyze simulated trajectories using tools that come with the packages;
  •     make an informed choice about which of the codes fits their needs best

Membrane Simulation

© Erik Lindahl