Date: Monday 10 – Thursday 13 June 2019
Venue: KTH Main Campus, Stockholm, Sweden – How to get here
Application opens: 1st March 2019
Application deadline: Friday 1st June 2019
Participation: First-come, first-served
Registration fee: Free. However, participants will need to cover their own accommodation and transport costs.

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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, the leading European Center of Excellence for Computational Biomolecular Research, is bringing together for the second time the main developers of some of the most popular and well-known applications for molecular modelling and simulations – GROMACS, AMBER, NAMD and VMD. The 2019 Seasonal School is funded and organized jointly with PRACE, the main HPC resource provider in Europe. The school is also supported by the Swedish National Infrastructure for Computing (SNIC).

Molecular modelling and simulations are integral part of biomolecular research. Yet, there is insufficient expertise on efficient usage of HPC resources among the user community. The current school is organized to fill that gap and builds on the very successful first edition of the event.

Over the 4 days of the event, the school program will allow participants to get a comprehensive understanding of the  usage of the different codes; their scalability and performance, as well as ways to avoid potential issues; and learn the best practices about using them on HPC systems. Extensive hands-on sessions will cover more than half of time during the school.

Please note that participants must have prior experience with one or more of the applications (GROMACS, NAMD or AMBER). The course does not include a general introduction to MD simulation methods.

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 program is free of charge but participants are responsible for own travel and accommodation costs. During the hands-on sessions participants can use own laptops, provided that all the required software is installed prior to the event. A detailed list of needed applications will be communicated in advance.

Both academic and industrial researchers residing in PRACE member countries, European Union Member States or Associated Countries, are welcome to apply to attend the school. All lectures and training sessions will be in English.

Registration Opening: 1st of March 2019.

No participation fee.

Please note that the number of places is limited, so register early to ensure a place.

Additionally, BioExcel CoE will be providing a limited number of travel bursaries for a fixed amount (€120 per day of the course) for this event.

If you would like to be considered for a travel bursary, please contact Michelle Mendoca. Please note that the travel grants will be awarded on a competitive basis and additional documentation, such as a letter of support and a biography, will be requested during the application process. More details about the travel bursary can be found here.


Prof. Thomas CHEATHAM (University Information Technology, University of Utah) – main developer of AMBER
Joao RIBEIRO (University of Illinois, Urbana-Champaign) – developer of NAMD and VMD
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 June 2019
08:30-09:00  Registration
09:20-09:40  Welcome  Lilit Axner
09:40-10:00  BioExcel Center of Excellence  Rossen Apostolov
10:00-10:30  Coffee break
10:30-12:00  Molecular visualisations with VMD (ppt)  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 (zip)
 15:00-15:30  Coffee break
 15:30-17:30  Hands-on VMD (pdf)
 15:30-17:30  Welcome dinner
Day 2 – Tuesday 11th June 2019
 09:30 – 10:30  HPC Simulations with NAMD (pdf-1)  Joao Ribeiro
 10:30 – 11:00 Coffee Break
11:00 – 12:00  HPC Simulations with NAMD (pdf-2)
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 June 2019
 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
Day 4 – Thursday 13th June 2019
 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