Avoiding Model Instability: How to Check if Your Energy Minimization Actually Worked

When working with molecular systems in GROMACS, energy minimization is a critical step to eliminate steric clashes and create a geometry that’s suitable for molecular dynamics. But how can you be sure it’s actually done properly?

If you’ve ever launched an energy minimization run and moved on to equilibration, only to experience unexpected crashes or erratic trajectory behavior, it could be that your minimization step didn’t really converge. Fortunately, if you’re using the GROMACS Wizard in SAMSON, there are clear ways to verify that your system is safe to proceed.

Key Indicators: Epot and Fmax

The two main indicators of a successful energy minimization are:

  • Potential energy (Epot): This should be negative and, for a solvated protein, typically in the range of -105 to -106. A downward trend showing convergence is what you want to see.
  • Maximum force (Fmax): This should be below your specified threshold (usually set in the emtol parameter). For example, emtol = 1000.0 means Fmax should not exceed 1000 kJ mol⁻¹ nm⁻¹.

These values are displayed at the end of the energy minimization output. You can access this in the GROMACS Wizard’s Output window:

Output

What if Fmax > emtol?

If your Fmax remains above the threshold even though the energy decreased, it means that convergence wasn’t reached. Sometimes that’s acceptable—but it can make your system unstable. In that case, you have some options:

  • Increase the nsteps parameter to extend the minimization time.
  • Change the integrator type if needed, e.g., from steep to cg (conjugate gradient).
  • Use the final structure from this minimization run as input for a second minimization pass.

Follow the Plot 📉

To visualize how the energy evolved, check out the plot at the bottom of the GROMACS Wizard tab. A steady convergence of Epot shows that your minimization proceeded smoothly.

Minimization plot

If your energy oscillates or flattens too early, that’s a signal to revisit your parameters. To explore other minimization settings, click the All… button in the Advanced Parameters panel and adjust fields like emtol, emstep, or integrator.

Conclusion

Energy minimization isn’t just a checkbox—it’s a foundational step for simulations. Taking time to verify its success will save you debugging time later and make your simulations more reliable. Whether you’re running a simple system or preparing for lengthy dynamics, understanding the outputs of your minimization step in SAMSON’s GROMACS Wizard is well worth the effort.

To learn more, visit the official documentation page: Energy Minimization in the GROMACS Wizard.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.

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