What to Look For After Energy Minimization in GROMACS Wizard

Energy minimization is a key step in the molecular dynamics workflow. It helps to remove steric clashes or geometric problems in your molecular model before moving on to more computationally intensive stages like equilibration and production runs. But after clicking the Minimize locally button in the GROMACS Wizard in SAMSON, how can you confidently assess whether the minimization was successful?

This post focuses on understanding how to import, analyze, and evaluate results once a molecular system has been minimized with GROMACS Wizard. If you’ve ever hesitated before moving to the next simulation step, unsure whether your structure is stable enough, this is for you.

Step 1: Import the Right Data

After a successful local minimization, a pop-up will ask how you’d like to import the results. You can choose to:

  • Import the whole trajectory
  • Import only the last frame (recommended for minimization)
  • Pick a range of frames

You can also set options like using Periodic Boundary Conditions or centering on a specific part of your system, such as the protein.

Load the last frame

Step 2: Check the Plot

Right after importing, look at the plot in the Plots section. It shows the evolution of the potential energy (Epot) during minimization. A smooth downward curve that stabilizes is what you’re aiming for. It helps you visually confirm whether the system has converged.

Minimization plot

Click the Save button if you’d like to keep the plot for your records or reports.

Step 3: Evaluate Stability

This is the part where many users are unsure: how do you know if the minimization has truly worked?

  • Potential Energy (Epot): Should be negative and on the order of 105–106 kJ/mol for typical protein systems in water. A more negative value usually indicates a stable configuration.
  • Maximum Force (Fmax): This is reported in the Output window. It should be below your set emtol threshold (e.g. 1000 kJ/mol/nm). If it’s too high, the system might not be well relaxed.

Output

Common Issues and Quick Fixes

If Fmax stays above your threshold even if Epot seems converged:

  • Increase the maximum number of minimization steps
  • Re-run the minimization using the previous output
  • Change the emtol to a slightly higher value if justified
  • Try a different minimization algorithm (integrator) in the advanced parameters

Final Notes

Minimization is not just a box to check off—it’s a crucial validation step. By using GROMACS Wizard in SAMSON, you not only get an automated setup but also powerful visual and numerical tools to help you decide when it’s safe to proceed to simulation.

Learn more about the Energy Minimization step in the official documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.

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