9-11 October 2019
CSC - IT Centre for Science
Europe/Helsinki timezone

Workshop Objectives

The worshop will introduce HADDOCK (High Ambiguity Driven protein-protein DOCKing) which is an information-driven flexible docking approach for the modeling of biomolecular complexes, and PMX which is a service for users who need to do free energy calculations. PMX utilizes the Gromacs classical molecular dynamics simulation engine to perform calculations at the background. The workshop also covers advanced usage of Gromacs itself in particular on HPC environment.

Upon registration the participants are asked for special topics they are interested in which potentially could be covered at the workshop. It will be possible to follow a video stream of the lectures also remotely, but unfortunately we will not be able to support doing the hands-on remotely. Check closer to the event for detailed instructions, or contact us.


Please register for on-site or remote participation here. Registration deadline is 27th September 2019 by 12:00

BioExcel can provide a limited number of travel bursaries for participants. Instructions to apply can be found in the registration form.

Tentative Programme / to be updated

Wednesday, 9th October

12:00 Lunch
13:00 Gromacs - where are we now, what's new, what's coming in the future
13:30 Participant Introduction
14:00 Maximizing Gromacs performance for HTC and HPC
14:30 Hands on - Performance
15:00 Advanced simulation protocols in GROMACS
15:30 Hands on - Advanced simulation protocols
18:00 Light dinner and social program
21:00 End of Day 1

Thursday, 10th October

09:00 PMX - alchemical free energy calculation setup tools introduction
10:00 Hands on - PMX
12.00 Lunch
13:00 HADDOCK – Modelling intermolecular interactions
14:00 Hands on - HADDOCK
15:00 HADDOCK – advanced topics
17:00 End of Day 2

Friday, 11th October

09:00 Getting deeper into issues and questions that emerged during the workshop
10:00 Participant contributions
12:00 Closing

Speakers and organizers

  • Dr. Christian Blau, Theoretical and Computational Biophysic
    KTH Royal Institute of Technology

  • Dr. Rodrigo Vargas Honorato, Computational structural biology group
    Utrecht University

The event is organized in collaboration with BioExcel and CSC and supported by PRACE.

Language:  English

CSC - IT Centre for Science
Training room Dogmi, 1st floor
Life Science Center, Keilaranta 14, Espoo, Finland

How to reach us

CSC is located in Keilaniemi, Espoo, 10 km west of the Helsinki City Center. Detailed information is available here.


We recommend choosing a few hotels that are most close to our premises. The nearest hotel is Radisson Blu Espoo, which is in a walking distance (only 500 m) from CSC. Another hotel close to the venue (1,8 km) is Sokos Hotel Tapiola GardenOther hotels are located in Helsinki' downtown with a frequent and fast bus connection to Keilaniemi. Please note, that there are no special rates for participants at any hotels.

If you have any questions, please click on the support link on the left to send an e-mail to the local organizers.