Production MD: How Long Should a Protein-Ligand Simulation Run?

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

A practical guide to choosing MD simulation duration. Covers 10ns vs 50ns vs 100ns, when each is appropriate, and how to validate that your simulation has converged.

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

Key References

• Abraham, M.J. et al. GROMACS. SoftwareX 1-2, 19-25 (2015).
• Hospital, A. et al. Molecular dynamics simulations: advances and applications. Adv. Appl. Bioinform. Chem. 8, 37-47 (2015).

Scope & Limitations

Optimal duration depends on the biological question RMSD plateau is necessary but not sufficient for convergence Longer is not always better — check convergence metrics