Did Your Molecular Minimization Actually Work? Here’s What to Check

After going through the steps of energy minimization in molecular dynamics, it’s tempting to jump straight to equilibration and production runs. But wait — how do you know your energy minimization was successful? Many molecular modelers overlook this crucial verification step. Let’s take a closer look at two key indicators you can (and should) use to assess whether your system is truly ready to move forward.

Why post-minimization checks matter

Skipping the validation step after energy minimization can lead to issues in equilibration or simulation phases, costing time and potentially invalidating results. Even if GROMACS doesn’t report an error, the final state of the system might not be suitable for stability or exploratory studies.

Two quantities that tell the story: Epot and Fmax

When you finish the energy minimization using the GROMACS Wizard in SAMSON, it’s helpful to immediately look at two output values:

  • Potential energy (Epot): GROMACS reports this value at each minimization step. It should be negative, and for a typical solvated protein, it is usually on the order of 10⁵ to 10⁶ kJ/mol.
  • Maximum force (Fmax): This is compared against your chosen energy minimization tolerance (emtol). Ideally, Fmax should be less than the value you set in emtol. For example, if emtol = 1000.0, your last Fmax should be ≤1000 kJ mol−1 nm−1.

Here’s a typical output window, where these values are reported:

GROMACS output showing energy and force values

Not converging? Here’s what to tweak

Sometimes energy minimization will reach the maximum number of steps without hitting the desired Fmax threshold. This can happen even if Epot decreases nicely. Rather than pushing ahead, consider:

  • Increasing the maximum number of minimization steps: Sometimes your system just needs more time to converge.
  • Restarting minimization using the output of the previous run. The system may need another round to refine further.
  • Changing the minimizer (e.g., switching the integrator method) under advanced parameters.
  • Reducing step size to improve convergence in complex systems.

These options are easily controlled within the GROMACS Wizard in SAMSON. Just click on the All… button in the Parameters pane to access advanced settings:

Advanced minimization parameters

Bonus: Visual evaluation with plots

Besides numerical indicators, the GROMACS Wizard automatically generates a plot of potential energy over time. A smooth and steady descent is a good sign, while oscillations or plateaus might indicate deeper issues in the setup.

Minimization plot

Conclusion

If your minimization shows negative Epot and low Fmax, you’re likely in good shape to proceed. Taking the extra moment to validate can save a lot of downstream frustration. SAMSON’s GROMACS Wizard makes it easy to check these values and re-run if necessary, helping you make informed decisions about your molecular simulations.

Learn more and dive into the Energy Minimization documentation.

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

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