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
© Erik Lindahl
