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Introduction to GROMACS Workshop

Online SNIC/PRACE workshop in collaboration with BioExcel
Note: The times for the workshop are based on the Central European Summer Time (CEST) time zone (Stockholm).

Time: Thu 2020-09-03 09.00 - Fri 2020-09-04 16.00

Location: online

image of a biomolecular simulation as advertising for the Introduction to GROMACS Workshop

GROMACS  is a free, open-source and high-performance software suite for molecular dynamics simulation and analysis. This workshop will provide an introduction to using GROMACS.

After attending the workshop, participants should have the knowledge and skills to be able to perform molecular dynamics simulations and simple free energy calculations using GROMACS.  

The workshop will include online lectures and hands-on sessions on the following topics:

  • the basics of molecular dynamics simulations,
  • introduction to free energy calculations and
  • the capabilities of GROMACS.

During the hands-on computer practical sessions attendees will work on protein simulation and solving free energy problems using GROMACS.

The workshop is being run jointly by PRACE , the main high-performance computing (HPC) resource provider in Europe, BioExcel  (the leading European Centre of Excellence for Computational Biomolecular Research) and the Swedish National Infrastructure for Computing ( SNIC ).

Schedule

Thursday 3 September 2020 (Day I)

09:00-09:10 welcome
09:10-09:50 Erik Lindahl (topic TBA)
09:50-10:20 break
10:20-11:30 Alessandra Villa - Introduction to MD using GROMACS
11:30-13:00 break
13:00-14:30 Tutorial: Basic MD tutorial - Alessandra Villa and Artem Zhmurov
14:30-15:00 break
15:00-16:00 Szilárd Pall - Introduction to GROMACS parallelization and performance

Friday 4 September 2020 (Day II)

10:00-10:10 welcome
10:10-11:30 Berk Hess - Introduction to free energy calculations
11:30-13:00 break
13:00-14:30 Tutorial: Solvation Free Energy tutorial - Artem Zhmurov (Alessandra Villa)
14:30-15:00 break
15:00-16:00 Paul Bauer - GROMACS features and development

Speakers and Trainers

  • Paul Bauer (KTH Royal Institute of Technology)
  • Berk Hess (KTH Royal Institute of Technology)
  • Erik Lindahl (KTH Royal Institute of Technology)
  • Szilárd Páll (KTH Royal Institute of Technology)
  • Alessandra Villa (KTH Royal Institute of Technology)
  • Artem Zhmurov (KTH Royal Institute of Technology)

Chairs

Registration

For more information, including details of how to register, see events.prace-ri.eu/event/1033 .

Contact

If you have any questions about the workshop, please contact: