Tutorials

Here are some commonly available tutorial examples that you would adapt to run with this plugin. Before attempting the tutorials here, you need to have completed the steps in Installation and started the verdi daemon as described in Start/Stop AiiDA.

• Lysozyme in Water with aiida-gromacs
  • Software requirements
  • “AiiDA-fying” Lemkul’s tutorial
  • Viewing and sharing data
• genericMD CLI
  • GROMACS specific vs genericMD CLI process submissions
  • How to submit a process with genericMD
  • Another example to submit a process with genericMD
• Advanced Data Provenance - Coarse-grained setup of embedded GPCR
  • Introduction
  • Preparing the environment
  • Software and environment requirements
  • Aquiring and tidying up the receptor protein structure
  • Aligning PTH2R to a correctly orientated structure
  • Building a coarse-grained system from an atomic structure
  • Adding the membrane and solution around the protein with insane
  • Preparing the system for simulation
  • Continuing on to the MD simulation
    • Visualisation tools
    • Minimisation and equilibration steps
  • Acknowledgements