When working on molecular simulations, it’s common to reach the Energy Minimization (EM) phase and wonder: did it actually work?
While tools like SAMSON’s GROMACS Wizard streamline Energy Minimization, interpreting the outcome is still a step many modelers find ambiguous. Did the system really converge? Is this stable enough for production runs?
Here’s a breakdown of how to confidently verify your Energy Minimization results and avoid wasting time on unstable trajectories.
Start with the Output Window
After launching an EM calculation (locally or in the cloud), SAMSON’s GROMACS Wizard provides a detailed Output window that includes progress and final EM statistics. Two key metrics to focus on are:
- Potential energy (
Epot) - Maximum force (
Fmax)
These values are critical indicators of whether or not your minimization succeeded.
Understand the Metrics
Epot should be negative and of reasonable magnitude depending on your system size and composition. For a small protein in water, expect somewhere in the range of -10^5 to -10^6 kJ/mol.
Fmax is the maximum force on an atom. If it is below your threshold (as defined in the EM step, typically emtol = 1000.0), the system is considered minimized. If not, the system may still be unstable.
If Fmax > emtol at the end of minimization, here are some possible next steps:
- Increase the number of minimization steps and re-run.
- Reduce the minimization step size.
- Switch to a different minimization integrator.
Check the Plot to Visualize Convergence
In addition to printed numbers, GROMACS Wizard automatically generates a plot of Epot over the course of the EM steps. This is helpful to judge whether energy is steadily converging or fluctuating too much.
A declining and flattening Epot curve is a good sign. If the graph plateaus early or contains irregular spikes, it could be a sign of poor starting structures or unsuitable minimization parameters.
Avoid the Guessing Game
By checking both the numerical output (Epot and Fmax) and the visual plot, you avoid guessing whether your minimization worked. This is particularly important before running more computationally expensive simulation steps like equilibration or production MD.
To learn more about interpreting energy minimization results in SAMSON’s GROMACS Wizard and explore advanced parameter settings, visit the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/energy-minimization/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.