MD Simulation on Google Colab for Free: Complete Walkthrough

By BioDockify Computational Research Team · September 19, 2026 · Tutorial

Run molecular dynamics on Google Colab free: OpenMM and GROMACS setups, protein-ligand simulation cells, checkpointing against disconnects, and analysis export.

Read the complete article with tables, code and references on BioDockify.

Key References

• Eastman, P. et al. OpenMM 7. J. Chem. Phys. 28, 073902 (2017). DOI: 10.1063/1.4979247
• Abraham, M.J. et al. GROMACS. J. Chem. Phys. 143, 087101 (2015). DOI: 10.1063/1.4926576
• Google Colab FAQ. https://research.google.com/colaboratory/faq.html

Scope & Limitations

Free Colab caps GPU hours/day and disconnects idle sessions — production runs need checkpoint discipline No automatic analysis — export trajectories and analyze elsewhere (or use a managed platform)