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
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: