Programme

BIOEXCEL WORKSHOP BALKAN EDITION

ENHANCING BIOMOLECULAR SIMULATIONS WITH GROMACS, HADDOCK AND PMX

May 21-22, 2025, Sofia, Bulgaria

Day 1, May 21:

HADDOCK

8:30 – 9:30 Registration
9:30 – 9:45 Opening
9:45 – 10:00 EPICURE Application Support for EuroHPC Users
10:00 – 11:00 Lecture:
 Integrative modelling with HADDOCK, Alexandre Bonvin
11:00 – 11:15 Break
11:15 – 13:15 Practical session:
 HADDOCK tutorial on antibody-antigen modelling, Alexandre Bonvin & Vlad Cojocaru
13:15 – 14:15 Lunch break

Day 1, May 21:

GROMACS

14:15 – 15:15 Lecture:
 Molecular dynamics using GROMACS, Alessandra Villa
15:15 – 15:30 Break
15:30 – 17:00 Practical session:
 Tutorial: Introduction to Molecular Dynamics simulations, Cathrine Bergh
17:00 – 17:30 Break
17:30 – 18:30 Practical session:
 Tutorial: Enhanced sampling with AWH, Alessandra Villa
20:00 – 22:30 Social dinner

All indicated times are in the Eastern European Summer Time (EEST) zone (GMT +3)

Day 2, May 22:

PMX

10:00 – 11:00 Lecture:
 Alchemical free energy calculations with PMX/GROMACS, Bert de Groot
11:00 – 11:30 Break
11:30 – 13:00 Practical session:
 Tutorial on amino acid mutations with PMX, Bert de Groot
13:00 – 14:00 Lunch break

 

All indicated times are in the Eastern European Summer Time (EEST) zone (GMT +3)

Day 2, May 22

GROMACS performance

14:00 – 15:00 Lecture:
 Efficient use of CPU resources in GROMACS simulations, Andrey
Alekseenko
15:00 – 15:30 Break
15:30 – 17:00 Practical session:
 Efficient use of CPU resources in GROMACS simulations, Andrey
Alekseenko
17:00 – 17:30 Closing remarks

Day 3, May 23

Visit to Discoverer (optional)

11:00 – 12:00 Guided visit to the Bulgarian supercomputer “Discoverer” located in SofiaTechPark

Download Programme pdf

Key Topics Covered:

Gromacs introductory level and performance optimization
  • Molecular Dynamics Simulations:
    • Focus on GROMACS, learning how to set up MD simulations;
    • Enhancing configurational sampling with GROMACS by the Accelerated weighted histogram method;
    • GROMACS performance optimization.
HADDOCK 3.0 antibody-antigen docking introductory level
  • Using HADDOCK3 to model Antigen-Antibody interactions.
PMX introductory level
  • Free energy lecture and PMX tutorial on amino acid mutation.

Participants will receive personalized guidance from software developers and experts throughout the workshop. Attendees will enjoy enhanced support and in-person interaction with the trainers.

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BioExcel workshop Balkan edition

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BioExcel Balkan workshop

This project has received funding from the European High Performance Computing Joint Undertaking (JU) and Germany, Bulgaria, Austria, Croatia, Cyprus, Czech Republic, Denmark, Estonia, Finland, Greece, Hungary, Ireland, Italy, Lithuania, Latvia, Poland, Portugal, Romania, Slovenia, Spain, Sweden, France, Netherlands, Belgium, Luxembourg, Slovakia, Norway, Türkiye, Republic of North Macedonia, Iceland, Montenegro, Serbia under grant agreement No 101101903 and grant agreement No 101093290

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