Energy minimization is a crucial preparatory step in molecular simulations, especially before launching longer production runs such as molecular dynamics (MD). A poorly minimized system may result in unstable simulations, wasted computational resources, and misleading scientific conclusions.
Yet many modelers launch simulations right after minimization without verifying whether the system truly converged. If you’ve ever found yourself puzzled by sudden MD crashes or high forces during equilibration, this post is for you.
Why Minimization Convergence Matters
The goal of energy minimization is to reduce steric clashes and bring the system to a local energy minimum. While GROMACS Wizard makes the minimization process simple, the success of minimization isn’t just about watching the process finish. You need to check critical results to determine whether the minimization has really converged.
Where to Look: The Output Window
After launching energy minimization through the GROMACS Wizard (either locally or in the cloud), you can monitor progress in the Output window. This window provides detailed logs of the simulation, including potential energy at each step and the maximum force (Fmax) acting on any particle.
Key Metrics to Verify
- Potential Energy (Epot): This should be negative and typically on the order of 105 to 106 for a typical solvated protein. A steady decrease signals proper convergence.
- Maximum Force (Fmax): Compare this with
emtol, the energy minimization tolerance parameter. For example, ifemtol = 1000.0, then ideallyFmaxshould be under 1000 kJ mol-1 nm-1 at the end of the minimization.
Both values are displayed at the end of the minimization output.
Plotting the Progress
GROMACS Wizard automatically creates a plot showing the evolution of the potential energy (Epot) over the minimization steps. This is incredibly helpful for visually confirming that minimization proceeded smoothly.
In a good minimization, you should see a smooth downward trend and eventual convergence. A jagged or abruptly terminating plot may indicate issues such as a too-low step limit or problematic structure.
Common Issues and What to Do
Sometimes, minimization may halt with Fmax > emtol. This means your system didn’t converge fully, even if Epot seems reasonable. In such cases:
- Increase the maximum number of minimization steps.
- Use the final structure from this run as the starting point for a new minimization.
- Adjust minimization parameters like the integrator or step size via the advanced options.
Takeaways
Spending a minute to examine your minimization output can save you hours of troubleshooting later. Look at the Epot, confirm Fmax is below your threshold, and examine the plot. If something looks off, it probably is.
To learn more, visit the official documentation page.
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