Still Getting High Forces After Energy Minimization? Here’s How to Check Convergence in SAMSON’s GROMACS Wizard

A common frustration in molecular modeling is thinking you’ve completed an energy minimization — only to discover later that steric clashes or unrealistic geometries persist. To make the most of your GROMACS runs, it’s crucial to verify that the system has really converged. Fortunately, SAMSON’s GROMACS Wizard makes verifying convergence both visual and straightforward.

Whether you’re preparing a molecular system for simulation or running batch jobs, knowing *when* minimization is sufficient is key. Here’s how you can effectively interpret the results of the energy minimization step in the GROMACS Wizard and avoid wasting compute time on unstable systems.

Why Convergence Matters

Energy minimization is your first line of defense against model instability. By reducing steric overlaps and ensuring appropriate geometry, you prepare the system for the next stages: equilibration and production simulations. But completing a minimization run doesn’t always mean success — especially if you don’t check a few key indicators.

Two Key Metrics to Watch

After your GROMACS Wizard minimization run finishes, head to the Output window and look for:

  • Potential Energy (Epot): Should generally be negative, often around 105-106 kJ/mol for protein-water systems. A steady decrease throughout the steps is a sign of healthy convergence.
  • Maximum Force (Fmax): This value should drop below your target threshold (usually set by emtol in the parameters). For example, emtol = 1000.0 means you’re aiming for Fmax < 1000 kJ mol^-1 nm^-1.

These values appear both during the process and explicitly at the end of the calculation log. Keep an eye on them to evaluate if your system is really settled or needs further effort.

A Quick Visual Check: The Plot

Scroll to the bottom of the Minimize tab to see the evolution of potential energy over the EM steps. A clean, downward trend often indicates that the system geometry is improving.

Minimization plot

You can save plots for documentation or comparison purposes using the Save button next to the figure.

What If It Hasn’t Converged?

If Fmax hasn’t dropped below the target or if the energy profile plateaus early, your system might still have issues. Some useful next steps:

  • Increase the maximum number of minimization steps
  • Decrease minimization step size for more gradual changes
  • Try a different integrator (e.g., switch from steep to cg)
  • Run a second minimization using the output of the first

If this seems overwhelming, don’t worry — you can adjust these in the Advanced Parameters popup in just a few clicks:

Advanced parameters

Summary

Running energy minimization is only half the job — interpreting the results ensures your system is stable and ready for the next steps. With SAMSON’s GROMACS Wizard, this process becomes both accessible and transparent. Take time to verify Epot and Fmax, check your plot for a steady drop, and know what to adjust if things don’t go as expected.

To learn more, visit the full step-by-step guide in the documentation: Energy Minimization with GROMACS Wizard.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.

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