Date: Monday 10 – Thursday 13 April 2017
Venue: KTH Main Campus, Stockholm, Sweden – How to get here
Application opens: 23rd January 2017
Application deadline: Friday 17th March 2017
Participation: First-come, first-served
Contact: Vera Matser
Registration fee: £0, participants will need to cover their own accommodation and transport cost

BioExcel will be providing a limited number of fixed amount travel bursaries for this event. If you would like to be considered for a travel bursary please indicate this during the application process. Eligibility criteria and conditions for the travel grants are available here.


BioExcel Center of Excellence is 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 is organized jointly with PRACE, the main HPC resource provider in Europe. The 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).


Prof. Thomas CHEATHAM (University Information Technology, University of Utah) – main developer of AMBER
Jim PHILLIPS (University of Illinois, Urbana-Champaign) – main developer of NAMD
erik-lindahl Prof. Erik LINDAHL (Stockholm University) – main developer of GROMACS
John STONE (University of Illinois, Urbana-Champaign) – main developer of VMD


Time Topic Trainer
Day 1 – Monday 10th April 2017
08:30-09:00  Registration
09:00-09:15  Welcome  Michaela Barth
09:15-10:00  BioExcel Center of Excellence – Training Programme  Vera Matser
10:00-10:30  Coffee break
10:30-12:00  Molecular visualisations with VMD  John Stone
12:00-13:00  Lunch
13:00-13:45  How to use the PDC Supercomputing systems Henric Zazzi
 13:45-15:00  Hands-on VMD
 15:00-15:30  Coffee break
 15:30-17:30  Hands-on VMD
 15:30-17:30  Welcome dinner at Syster o Bror
Day 2 – Tuesday 11th April 2017
 09:30 – 10:30  HPC Simulations with NAMD  Jim Phillips
 10:30 – 11:00  Group Photo and Coffee Break
11:00 – 12:00  HPC Simulations with NAMD
12:00 – 13:00  Lunch
13:00 – 14:30  Hands-on NAMD
14:30 – 15:00  Coffee Break
15:00 – 17:00  Hands-on NAMD
Day 3 – Wednesday 12th April 2017
 09:30 – 10:30  HPC Simulations with GROMACS  Erik Lindahl
 10:30 – 11:00  Coffee Break
11:00 – 12:00  HPC Simulations with GROMACS
12:00 – 13:00  Lunch
13:00 – 14:30  Hands-on GROMACS
14:30 – 15:00  Coffee Break
15:00 – 17:00  Hands-on GROMACS
18:00  Guided tour and Dinner at Vasa Museum
Day 4 – 13th April 2017
 09:30 – 10:30  HPC Simulations with AMBER  Tom Cheatham
 10:30 – 11:00  Coffee Break
 11:00 – 12:00  HPC Simulations with AMBER
 12:00 – 13:00  Lunch
 13:00 – 14:30  Hands-on AMBER
 14:30 – 15:00  Coffee Break
 15:00 – 15:15  Course Feedback
 15:15 – 17:00  Hands-on AMBER

How to apply

The course is free of charge (though you are responsible for your own travel and accommodation costs). For the hands-on sessions, participants can bring their own laptops, in that case you have to make sure that all the required software (a detailed list including expected versions will be communicated in advance) is installed once the course starts.

Full details and registration via the PRACE website

For more information on the BioExcel travel grant, please email Vera Matser