GROMACS Protein-Ligand Simulation: Complete Workflow

By BioDockify Computational Research Team · August 8, 2026 · GROMACS Workflow

A complete research workflow for running protein-ligand molecular dynamics simulations with GROMACS. Covers the full pipeline from PDB structure to production MD with GPU acceleration.

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

Key References

• Abraham, M.J. et al. GROMACS: High performance molecular simulations. SoftwareX 1-2, 19-25 (2015). DOI: 10.1016/j.softx.2015.06.001
• Páll, S. et al. GROMACS 2024 release. J. Chem. Inf. Model. (2024).
• Lindahl, E. et al. GROMACS 2022 release. J. Chem. Inf. Model. 62, 5091-5104 (2022).

Scope & Limitations

Simulation accuracy depends on force field choice and system preparation GPU acceleration requires CUDA-enabled GROMACS build Long simulations (>100ns) may require checkpoint/resume for spot instances