Molecular dynamics samples a model of molecular motion under explicit force-field and simulation assumptions. Define the observable and timescale you need before selecting an engine or trajectory length.
Choose the representation
Use GROMACS or OpenMM for supported atomistic workflows. Martini OpenMM provides coarse-grained modeling; bead-level behavior should not be interpreted as atomistic detail.
Review supported molecules and parameterization requirements. Metals, modified residues, covalent ligands, membranes, and unusual chemistry can require treatment beyond ordinary structure repair.
Prepare and equilibrate
Retain the correct assembly, molecular states, solvent, ions, boundary conditions, and force-field settings. Review minimization and equilibration before analyzing production dynamics. A simulation that runs is not necessarily a scientifically appropriate system.
Record ensemble, temperature, pressure, timestep, duration, restraints, and sampling outputs. Start with a pilot and review runtime and credit planning.
Analyze motion and convergence
MDAnalysis Trajectory Analysis supports trajectory interpretation. Ensure the topology and trajectory describe the same atoms in the same order. Check alignment, periodic boundaries, and selection before interpreting RMSD, RMSF, contacts, or other observables.
A stable RMSD alone does not establish thermodynamic convergence. Compare relevant observables across time windows and independent runs when the research decision requires it.
Compare energetics carefully
gmx_MMPBSA estimates end-state binding energies for compatible systems. OpenFE Relative Binding Free Energy supports alchemical comparisons under a different set of assumptions.
Do not interchange docking scores, end-state estimates, and alchemical free energies. Preserve topology, trajectory, setup, analysis choices, and uncertainties. Use computational evidence to focus the next experiment rather than claiming measured affinity from one trajectory.