If you’re setting up molecular dynamics simulations, one of the essential – yet often underestimated – preprocessing steps is energy minimization. Skipping it, or doing it incorrectly, may lead to steric clashes, unrealistic geometries, or unstable simulations downstream.
Fortunately, the SAMSON GROMACS Wizard simplifies this process, allowing you to efficiently perform energy minimization using pre-configured or custom parameters. Let’s walk through how to minimize your system and what to check to ensure that it converged properly.
Why energy minimization matters
Before running molecular dynamics (MD), the geometry of your structure might not be ideal. Bond lengths or angles might deviate from equilibrium, and atoms might overlap, creating unrealistic interactions. Energy minimization reduces the system’s potential energy by relaxing the geometry, which improves stability during the actual simulation phase.
Launching energy minimization
In the SAMSON GROMACS Wizard, switch to the Minimize tab to get started.
Here, you can provide either:
- A .gro file from a previous step, like system preparation
- A batch project path for processing multiple structures
To streamline your workflow, click the auto-fill button 
to automatically populate the input path from a preceding step:
Choosing minimization parameters
Default minimization parameters are provided, including the commonly adjusted emtol value (energy tolerance). You can leave them as-is or tweak them depending on your system.
Need more control? Click on the All… button 
to access advanced settings.
Running and checking the minimization
You can choose to run computations on your machine (Minimize locally), in the cloud, or just prepare input files:
- Generate inputs
- Minimize locally
- Minimize in the cloud
After the run, you’ll get a pop-up asking how to import the results. You can choose to view the entire trajectory or just the final frame—sufficient in many cases.
What makes a minimization successful?
Once complete, check:
- Potential energy (
Epot) – should be negative, around 105–106 for proteins in water. - Maximum force (
Fmax) – should be belowemtol, the force tolerance you set.
If Fmax exceeds emtol after the allowed number of steps, consider rerunning the minimization with updated parameters or a smaller step size.
Visualizing convergence
The Wizard also gives you a quick visual cue through plots of potential energy over the minimization steps, available in the Plots section at the bottom of the tab:
This plot can be saved if needed, particularly helpful when documenting or sharing your workflow.
Whether you’re a beginner or an experienced modeler, the GROMACS Wizard in SAMSON helps prevent early-stage simulation pitfalls by making energy minimization both accessible and configurable. You can learn more on the documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.