When Energy Minimization Doesn’t Converge: What to Check Before Giving Up

In molecular dynamics simulations, the Energy Minimization (EM) step helps relieve atomic clashes and brings the system to a physically realistic starting point. It’s often one of the first steps after preparing your system, but sometimes it just won’t converge—and that can be frustrating.

If you’ve struggled with this, you’re not alone. One common issue faced by molecular modelers is that Energy Minimization stops before reaching the target maximum force threshold (Fmax), even when the potential energy (Epot) seems reasonable. If this happens, your system might not be stable enough for the next steps like equilibration and molecular dynamics simulation.

Signs That EM Didn’t Converge

After running minimization, check two key outputs:

  • Potential Energy (Epot): This should be negative and show steady convergence over the minimization steps. For protein-in-water systems, it’s usually in the range of 105-106.
  • Maximum Force (Fmax): If Fmax remains higher than your configured threshold (e.g., emtol = 1000.0), SAMSON will note convergence failure.

Both are shown in the Output window, per step and summarized at the end:

Output

Now what? Useful troubleshooting options 👇

1. Increase Minimization Steps

If Fmax is close to your emtol threshold, simply increasing the maximum number of minimization steps might help. In SAMSON’s GROMACS Wizard, open the advanced parameters by clicking the All… button:

Advanced parameters

Then set nsteps to a higher value and try running the minimization again.

2. Restart from the Previous EM Output

You can rerun minimization using the output from the last EM attempt. Use the Auto-fill button to quickly load the GRO file from the previous step:

Auto input

3. Adjust Parameters Like Step Size or Integrator

Sometimes, you may need to reduce the step size or change to a more stable integrator. These settings are also available in the Advanced parameters section. Refer to tooltips inside the SAMSON interface for details or load custom parameters using an MDP file.

4. Visual Inspection

Before rerunning, quickly check your structure for issues such as clashing atoms or poor geometries. Sometimes, faulty protonation states or misaligned water boxes are the cause of instability.

Energy Plots Help Too

Don’t forget to scroll down to the Plots section to visualize how Epot evolves over time:

Minimization plot

This helps you see whether the system is smoothly converging or stuck early on.

Final Word

Energy Minimization might not always succeed on the first try, but equipped with the right tools in SAMSON’s GROMACS Wizard, you can identify and address the cause. Whether you increase steps, tweak parameters, or double-check your input structure, it’s worth taking a moment before rushing forward.

To learn more about the Energy Minimization step and related workflows in SAMSON, visit this documentation page.

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

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