BioExcel workshop

BioExcel workshop on GROMACS and HADDOCK

  • Date: October 18 – 19, 2023
  • Venue: Faculty of Natural Sciences, Ilkovičova 6, Bratislava
  • Format: hybrid, but in-person attendance is recommended for better learning experience
  • Hands-on workshop
  • Participation free of charge

National Competence Centres for HPC in Slovakia, Austria, Czechia and Hungary, together with BioExcel – Centre of Excellence in HPC are organizing a 1,5-day workshop focused on GROMACS software package. Focus will be on basic usage and deployment on GPU-accelerated HPC systems, the agenda will also cover more of the core modules for GROMACS developed by BioExcel (Haddock or PMX).

The workshop will take place in Bratislava, which can be reached conveniently from all involved countries: Slovakia, Czechia, Austria and Hungary. Participants from the rest of the EuroCC network are welcome, too! The event is organized in hybrid format, however, in-person participation is strongly encouraged. Attending in-person will allow you to get the most of the workshop, to interact closely with the lecturers during the lectures and practical exercises – simply to learn more!

Registration is closed

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ABOUT BIOEXCEL

BioExcel is the leading European Centre of Excellence for Computational Biomolecular Research. It is a major research and innovation hub for scientific computing, developing some of the most popular applications for modelling and simulations of biomolecular systems. BioExcel was established in 2015 and is now supported by the Horizon Europe programme.

Its mission is to accelerate the development and usability of the most widely used European open-source software for computational biomolecular research: GROMACS for molecular dynamics simulations; HADDOCK for integrative docking; PMX for free energy calculation preparation, and ensure that this continues to achieve significant impact in the international HPC landscape. These applications can be used with a range of pre-/post-processing tools within user-friendly workflows and container solutions. The software stack comes with great performance and scalability capabilities for extreme-scale utilization of the worlds largest high-performance computing (HPC) and high-throughput computing (HTC) compute resources.

BioExcel collaborates closely with the European High Performance Computing Joint Undertaking (EuroHPC JU) and participating member states – and the network of the National Competence Centres for HPC.

ABOUT GROMACS and HADDOCK 

GROMACS is one of the major software packages for the simulation of biological macromolecules. It is aimed at performing the simulation of large, biologically relevant systems, with a focus on both being efficient and flexible to allow the research of a number of different systems.

It is also one of the most widely used scientific software packages in the world, it is the largest free software and open source application in biomolecular research, and the only one of the major molecular dynamics simulation packages where development is led in Europe. GROMACS can use thousands of cores and hundreds of accelerators efficiently in parallel, enabling researchers to study large and complex biomolecular systems using supercomputing infrastructures.

HADDOCK is a versatile information-driven flexible docking approach for the modelling of biomolecular complexes. HADDOCK distinguishes itself from ab-initio docking methods in the fact that it can integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both. HADDOCK supports the incorporation of data from NMR and other biophysical methods, e.g. MS cross-linking and mutagenesis data, to drive the modelling process and the use of SAXS and IM-MS data to filter docking solutions.

PROGRAMME

18th October GROMACS

9:00 – 9:05 Welcome
9:05 – 9:10 BioExcel Introduction
9:10 – 9:45 Introduction to molecular dynamics simulation and GROMACS (part I)
9:45 – 10:00 Q&A
10:00 – 10:30 Introduction to molecular dynamics simulation and GROMACS
10:30 – 10:45 Q&A
10:45 – 11:15 Break
11:15 – 12:45 Tutoriál GROMACS: Protein-Membrane
12:45 – 14:00 Lunch
14:00-14:30  Running GROMACS on CPU and GPU
14:30 – 14:45 Q&A
14:45 – 15:15 Hands-on
15:15-15:45  Break
15:45 – 16:30 Hands-on
18:00 Social dinner (Sky bar restaurant (7th floor), Hviezdoslavovo námestie 7, Bratislava)
Trainers Alessandra Villa, Catherine Bergh, Farzaneh Jalalypour

19th October HADDOCK

09:00 – 10:30 Integrative modelling with HADDOCK
10:30 – 11:00 Break
11:00 – 12:45 Tutorial - HADDOCK
12:45 – 14:00 Lunch
Trainers Rodrigo Vargas, Alexander Bonvin, Marco Giulini

PRACTICAL INFO & TRAVEL

The event will take place at the Faculty of Natural Sciences of Comenius University in Bratislava in room CPS+ (room number is B1-322).
Faculty address: Mlynská dolina, Ilkovičova 6, 842 15 Bratislava.
GPS : 48°09’00,12″ | 17°04’17,85″

Access to workshop venue and programme is free of charge for registered participants. Light meals and coffee breaks will be provided by the local organizers.

You will need your own laptop to be able to participate in the hands-on parts. HPC system Devana will be used for the workshop. Access information and instructions will be provided shortly before the workshop.

How to get to Bratislava

BY PLANE: Bratislava Airport (BTS)

There are direct flights to a number of destinations in Europe and a number of airlines operate their direct routes to Bratislava. Bratislava airport can be reached from the city centre in 15–20 minutes. To get to the city center you can take a taxi – do not forget to ask about the price in advance or use HOPIN mobile app. If you travel on the budget,  take the bus no. 61 to the main train station. From here, you can walk to the city centre in 15 minutes or take bus no 93 (exit Hodžovo námestie) or tram no 1 (exit Námestie SNP). Bus tickets are available from ticket machines at bus stops or in kiosks. The tickets which cost around EUR 1 must be validated in the buses.

BY PLANE: Vienna – Schwechat Airport (VIE)

The airport at Vienna-Schwechat is only 40 kilometres west of Bratislava and it is one of the main gateways to Slovakia. Buses to Bratislava depart at 30 to 60-minute intervals. Tickets can be bought on the bus; chceck the following companies slovaklines.sk, regiojet.com, flixbus.com.

BY TRAIN: ZSSK – Slovak National Carrier

Bratislava connects to the main lines from Prague, Budapest, Vienna and various regions in Slovakia. The Bratislava Main Station is well connected to the rest of the city via trams, buses or trolleybuses and you can get to the Old Town on foot in only 15 minutes. From the train station in Petržalka, the no. 80, 91, 93 buses take you to the city centre.

BY TRAIN: RegioJet

The RegioJet carrier provides connection to Prague, Brno and Pardubice.

BY BUS:

Bratislava is also conveniently connected with many European cities via a network of bus lines. It has frequent service to the surrounding areas and also to other regions in Slovakia. Buses arrive and depart from Mlynské Nivy bus station. Coaches between Bratislava and Vienna run at one-hour intervals.

Useful links:

Slovaklines

regiojet.com

flixbus.com

BY CAR:

Bratislava is situated at the intersection of several important motorways. The distance to Prague is 330 km, Budapest 200 km and Vienna 65 km. If you are bringing your own car, you need to have a valid electronic vignette to use the specified sections of motorways and expressways. The vignette is related to a specific time period regardless of the distance driven or the number of journeys. The minimum validity period is ten days (costs around EUR 10). HERE.

Information sourced from visitbratislava.com where you can find plenty more useful tips for getting around Bratislava.

Where to stay in Bratislava

Diverse hotels, hostels, guest houses and private accommodation can be booked via standard providers – check e. g. Trivago or booking.com.

There are a few hotels near the faculty:
Hotel Sorea Regia
How to get from the hotel to the faculty? => Take tram number 9 from the stop Kráľovské údolie to the stop Botanická záhrada, then walk for 13 minutes.

Hotel Devin
How to get from the hotel to the faculty? => Take tram number 4 from the stop Most SNP to the stop Riviera, then walk for 13 minutes.

Grand Hotel River Park
Ako sa dostať z hotela na fakultu? => Električka č. 4 zo zastávky Chatam Sófer na zastávku Botanická záhrada + 12 minút pešo.

Hotel Družba
Hotel Družba is a budget accomodation for students. The hotel is located 1.1 km from the faculty (14 minutes walk).

Training materials:

Introduction to molecular dynamics simulation and GROMACS: 

https://zenodo.org/records/10017516

Running GROMACS on CPU and GPU: 

https://zenodo.org/records/10017683 

Tutorial “GROMACS Protein-Membrane / Introduction to Membrane-Protein Simulation”:
https://tutorials.gromacs.org/membrane-protein.html

Tutorial “Running GROMACS on CPU and GPU”:
https://hackmd.io/@M6Ldm9LPQ1CAIclMXIVZKA/BkyDpLux6

Integrative modelling with HADDOCK:

https://www.dropbox.com/scl/fi/54w6n9tapuaj4jhmjf27r/2023-10-HADDOCK-BioExcel-Bratislava.pdf?rlkey=fringazzci8o0gdcnbl8aw219&dl=0