Workshop: Setting up and running simulations in Gromacs


Jupyter notebook

Required software and resources

Learning resources


Perform a short MD simulation for a protein of your choice in Gromacs. Expect, that an arbitary chosen protein structure may not be well suited for straightforward simulations. It may have partially unresolved residues, ligands, etc. Seek advice in advance via Slack.

  1. Present snapshots of system before and after simulations.
  2. Include plots of energy, temperature, box size versus simulation time.

Suggested problem sets

Each student should take a unique PDB structure at his/her own discretion.