A molecular structure can finish energy minimization and still leave you with an important question: is it actually ready for equilibration? A falling energy plot is encouraging, but it does not tell the whole story. Checking both the potential energy and maximum force helps you distinguish a useful relaxation from a run that stopped before meeting its target.
Energy minimization is a preparatory step: it relaxes steric clashes and poor local geometry before equilibration. In GROMACS Wizard, the key is not just to launch the job, but to review its outputs before moving on.
Start with the energy plot
After the job finishes and its results are loaded, look at the Plots section at the bottom of the Minimize tab. The plot shows the system’s potential energy, Epot, over the minimization steps. A steady downward trend, like the example below, is a useful sign that the structure is relaxing.
But don’t use the shape of the plot as your only pass/fail test. The output also reports the final potential energy and maximum force, and both are worth checking before you continue.
Check the two values that matter
- 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 as context, not a universal cutoff: systems differ. - Maximum force (
Fmax): compare this with the target set byemtolin the advanced parameters. For example,emtol = 1000.0specifies a targetFmaxno greater than 1000 kJ mol-1 nm-1.
You can find these values in the Output window, where they are written during the run and at the end. The screenshot below shows the kind of output to inspect.
A useful review routine is to check the final output first, then look at the energy plot for context. That way, a visually smooth curve does not distract you from a maximum force that remains above the specified target.
What if the target wasn’t reached?
A run can reach the maximum number of minimization steps and produce a reasonable-looking Epot while still ending with Fmax > emtol. In that case, don’t assume the system is ready for further equilibration or simulation just because the energy decreased. The minimization target has not been met, so investigate before proceeding.
Possible next steps described in the tutorial include increasing the number of minimization steps, reducing the minimization step size, or changing minimization parameters such as the integrator. You can also run minimization again using the previous minimization result as the input. If you adjust parameters, make the change deliberately and check the output again rather than relying on the plot alone.
Keep the result you need
When importing results, you can choose the whole trajectory, only the last frame, or a range of frames, along with options for periodic boundary conditions and centering. For a quick continuation, importing the last frame is one available choice. If you cancel the import prompt, the results are not deleted, and the plot is still generated. Results are also available in the configured results folder; energy-minimization folders have the suffix _em.
Once Epot and Fmax are acceptable for your system, continue to Step 3: NVT Equilibration. For the full workflow and interface details, learn more in the Energy Minimization tutorial.
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