A minimization run finishes, the energy plot slopes downward, and the structure looks calmer. Is it ready for equilibration? That is a common—and important—question for molecular modelers. A reassuring plot is useful, but it should not be the only check: the final potential energy and maximum force tell you more about whether the minimization met its target.
Energy minimization is an early relaxation step. It helps address steric clashes and poor local geometry before equilibration, but a completed job does not automatically mean the system is ready to move on. Here is a practical way to review the result in GROMACS Wizard.
Start with the energy plot, then check the numbers
After the job finishes and results are loaded, GROMACS Wizard generates a plot of potential energy (Epot) over the minimization steps. A steady decrease is a useful sign of convergence. The plot is also saved automatically, and in batch projects a plot is generated for each subproject. Use the Save button above the figure if you want to keep a copy.
Next, inspect the output for two values: Epot and Fmax. The output reports them per step and at the end of the run, and you can review it in the Output window.
- Potential energy (
Epot): It should be negative. For a simple protein in water, the documentation gives an approximate scale of 105–106, depending on system size and the number of water molecules. Treat that range as context, not a universal pass/fail threshold. - Maximum force (
Fmax): Compare this with the target set byemtolin the advanced minimization parameters. For example,emtol = 1000.0sets a target maximum force no greater than 1000 kJ mol-1 nm-1.
When the run finishes but the force target does not
A minimization may reach its maximum number of steps and produce a reasonable-looking Epot, yet still have Fmax > emtol. That means the force target was not met. In this situation, do not treat a plausible energy or a completed job as proof that the system is ready for equilibration. The system may not be stable enough to continue, so investigate before moving on.
The documentation suggests several options to consider: increase the number of minimization steps, run minimization again using the previous minimization output as input, decrease the minimization step size, or change minimization parameters such as the integrator. These are choices to evaluate for your system—not automatic fixes. After another run, check the output values again.
A simple review routine
- Look at the
Epotplot for the overall energy trend. - Read the final
EpotandFmaxin the Output window. - Compare
Fmaxwith theemtoltarget used for the run. - If the force target was not reached, assess the setup and parameters before proceeding.
- Once the energy and maximum force are acceptable for your system, continue to NVT equilibration.
Keep the result and the route back
Results are available in the results folder specified in GROMACS Wizard. Launch folders are named with the date, time, and step description; minimization results use the suffix _em. If you choose not to import the trajectory, clicking Cancel in the import prompt does not delete the results, and the plot is still generated. For batch runs, check each subproject rather than assuming one result represents the whole batch.
The key takeaway: use the plot to understand the trend, but use both Epot and Fmax to judge whether minimization met its goal. For the full walkthrough, see the GROMACS Wizard energy minimization tutorial.
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