This course gives a practical introduction on how to run GROMACS MD simulations efficiently on modern hardware including both CPUs and GPUs. In addition to speeding up MD simulations, also workflow automation and advanced sampling techniques are discussed. CSC’s Puhti and Mahti supercomputers will be used for the hands-on exercises.

The course consists of lectures and hands-on exercises. GROMACS will be used in the exercise sessions.

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

Learning outcome

After the course the participants should have the skills and knowledge needed to efficiently use CPU and GPU resources in GROMACS simulations.

Prerequisites

The participants are assumed to have working knowledge of GROMACS, basic Python and Linux/Unix skills are required. The fundamentals of molecular dynamics or basic usage of GROMACS are not covered on this course. Please consult these materials, if you’re uncertain of your Python, Linux or GROMACS skills.

Agenda (NOTE: times are CET)

Day 1, Monday 1.2

• 9:00 – 9:30  Introduction, organization (TBA)
•  9:30 –11:30 QM/MM simulations with GROMACS and CP2K (Dmitry Morozov)
• 11:30-12:30 Lunch
• 12:30–14:00  Participant flash talks on their research and/or interests

Day 2, Tuesday 2.2

•  9:00–11:30  HPC workflows with GROMACS supported by BioBB – bioexcel building blocks / pycomms (Adam Hospital)
• 11:30-12:30 Lunch
• 12:30–14:00  GROMACS – Python down to the metal interface for in-memory toolchains with GROMACS (Eric Irrgang)

Day 3, Wednesday 3.2

• 9:00–10:30  pmx – free energy calculations or other of the above (Vytautas Gapsys)
• 11:30-12:30 Lunch
• 12:30–14:00 Performant setup  GROMACS on GPUs (Christian Blau)

Lecturers: 

• Dr. Christian Blau, Theoretical and Computational Biophysics, KTH Royal Institute of Technology
• Dr. Yuriy Khalak, Computational biomolecular dynamics group at the Max Planck Institute for Biophysical Chemistry, Göttingen
• Dr. Vytautas Gapsys, Computational biomolecular dynamics group at the Max Planck Institute for Biophysical Chemistry, Göttingen
• Dr. Adam Hospital, Molecular Modelling and Bioinformatics, Institute of Research in Biomedicine, Barcelona
• Dr. Eric Irrgang, Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville
• Dr. Dmitry Morozov, Department of Chemistry, University of Jyväskylä

Language:   English
Price:           Free of charge (3 half training days)

Materials: The detailed agenda, links to slides and exercises and all questions asked and answered during the workshop can be found at: https://a3s.fi/advanced_gmx/PRACE_CSC_BioExcelWorkshop-GROMACS_workflows_and_advanced_topics.html

REGISTRATION is OBLIGATORY since the details to access the online course will be provided to the registered and accepted attendees only. Participants will be selected based on skills, motivation and maximum coverage of research groups. If you have registered to this course and you are not able to attend, please CANCEL your registration in advance by sending an email to patc@csc.fi