GROMACS protein–ligand MD simulation workflow

Why run MD after docking?

Docking gives a static snapshot. Molecular dynamics (MD) simulates the motion of the complex in explicit water over time, showing whether the predicted pose stays bound and how the protein responds.

The workflow

1. Prepare the protein topology. Use gmx pdb2gmx with a chosen force field and water model. Check chain handling and missing residues first.
2. Parametrise the ligand. Generate ligand topology and parameters, for example with CGenFF or ACPYPE/GAFF2, and include them in the system topology.
3. Build the box and solvate. Define a periodic box with gmx editconf and add water with gmx solvate. Membrane proteins need a lipid bilayer built first.
4. Add ions. Neutralise the system and set physiological salt concentration with gmx genion.
5. Minimise the energy. Remove bad contacts with steepest descent until the maximum force converges.
6. Equilibrate in NVT then NPT. Stabilise temperature, then pressure and density, restraining the ligand and protein backbone so the system relaxes without drifting.
7. Run production. Run unrestrained MD for the planned length, for example 50 to 100 ns, writing frames at regular intervals.
8. Process the trajectory. Fix periodic boundary effects and centre the complex with gmx trjconv before analysis.

Tips that save time

• Inspect the minimised and equilibrated structure visually before starting production.
• Use checkpoint files so a crashed long run can resume.
• Keep force field, water model and ligand parameters consistent and documented.
• Check temperature, pressure, density and energy plots to confirm equilibration.

Next step

Once the run finishes, analyse stability and interactions. See how to interpret MD simulation results.

Frequently asked questions