GROMACS (www.gromacs.org) is a free, open-source and high-performance software suite for molecular dynamics simulation and analysis. The workshop aims to provide the basis to perform molecular dynamics simulations and simple free energy calculations using GROMACS.

The workshop is organized jointly by PRACE, the main HPC resource provider in Europe, BioExcel, the leading European Center of Excellence for Computational Biomolecular Research and SNIC, Swedish National Infrastructure for Computing.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
• The capabilities of GROMACS

During the hands-on computer practicals you will work on protein simulation and solvation free energy using GROMACS.

Prerequisites

The workshop is at beginners level and assumes no prior experience in GROMACS.

The participants need to have access to a computer where the following software were already installed: Jupiter notebook, GROMACS, VMD (visualisation), Xmgrace (plotting tool) to actively follow the tutorial.