A Lower Energy Isn’t the Whole Story: Checking Whether Minimization Is Ready to Move On

A molecular structure can finish an energy-minimization run and still leave you wondering: is it actually ready for equilibration? A falling energy plot is encouraging, but it does not tell the whole story. Before moving on, check both the potential energy and the maximum force. These two values help you distinguish a useful relaxation from a run that stopped before reaching its target.

Energy minimization is a preparation step: it relaxes steric clashes and poor local geometry in a prepared system. In the GROMACS Wizard, you can start from the GRO file produced by preparation or a previous minimization, or provide a prepared batch project. The auto-fill button can use the previous successful project as the input, which helps avoid selecting the wrong file.

Selecting the input for energy minimization

Use the plot as a trend, not a pass/fail test

After the job finishes and results are loaded, the Plots section shows how the system’s potential energy, Epot, changes over the minimization steps. A steady downward trend, like the example below, is a useful sign of convergence. But a plot alone cannot confirm that the minimization met its force target. Check the reported maximum force as well.

Potential energy convergence during minimization

Two checks before equilibration

  • Potential energy (Epot): It should be negative. For a simple protein in water, the documentation gives an approximate order of magnitude of 105–106, depending on system size and the number of water molecules. Treat this as context, not a universal pass/fail range: the system matters.
  • Maximum force (Fmax): Compare it with the target set by emtol in the advanced parameters. For example, emtol = 1000.0 sets a target maximum force no greater than 1000 kJ mol-1 nm-1.

Look for these values in the Output window. They are reported during the run and at the end, so you can check the final result against the target rather than relying only on the visual shape of the plot.

Energy and maximum-force values in the output

When energy looks reasonable but force is still too high

A run may reach its maximum number of minimization steps with a reasonable Epot, while still having Fmax > emtol. That means the energy value alone is not enough to decide whether the system is ready for the next stage. The documentation cautions that such a system may not be stable enough for further equilibration and simulation.

If the force target has not been met, review the setup rather than treating the energy plot as proof of success. Possible next steps include increasing the number of minimization steps, minimizing again from the previous minimization output, decreasing the step size, or changing minimization parameters such as the integrator. Which adjustment makes sense depends on the system and the run’s output.

A practical handoff checklist

  1. Confirm that you minimized the intended GRO file or batch project.
  2. Review the energy plot for its overall trend.
  3. Check the final Epot and Fmax in the output.
  4. Compare Fmax with the configured emtol.
  5. Continue to NVT equilibration only when the energy and force are acceptable for your system.

For batch work, the plot is generated for each subproject, so the same checks can be applied to individual systems rather than assuming that every member of the batch behaved identically. Results are stored in the configured results folder; energy-minimization folders have the suffix _em. You can also choose to import only the last frame, a range of frames, or the whole trajectory—the result files remain available even if you cancel trajectory import.

For the full workflow and parameter details, see the GROMACS Wizard energy minimization tutorial. When the checks are satisfactory, continue with Step 3: NVT Equilibration.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at samson-connect.net.

Comments are closed.