The frustration is familiar to many molecular modelers: you’ve built or downloaded a molecular structure, set everything up for a simulation, only to find out that your model contains steric clashes or non-ideal geometries that cause your simulation to crash before it really begins.
This is where Energy Minimization (EM) comes into play. It’s an essential pre-simulation step that helps relax your structure by removing energetically unfavorable contacts, such as overlapping atoms. But setting it up manually in GROMACS can be technical and time-consuming, especially when needing to fine-tune parameters or manage multiple files and paths.
The GROMACS Wizard in SAMSON makes this process more accessible and hassle-free—especially in Step 2, dedicated entirely to energy minimization. Here’s how it helps you streamline this important step, whether you’re working on a single structure or running batch jobs.
Step 1: Choose Your Input Smartly
When launching the EM step, you can provide either:
- A
.grofile prepared in the previous step - A batch project
But the real time-saver? Just click the auto-fill button 
to automatically load the last used file or project. No need to browse through folders or wonder which file to use.
Step 2: Tweak—or Trust—Your Parameters
Good news: you don’t need to be a GROMACS expert to start. The EM step comes preloaded with default parameters in the Minimize tab that work for most systems.
Want more control? Click All… to access advanced parameters, where you can:
- Adjust
emtol(the maximum force threshold) - Change the minimization algorithm
- Save or load settings from an
.mdpfile
Step 3: Run Locally or in the Cloud
Once configuration is done, click Minimize locally to begin the energy minimization on your PC. Have higher computational demands? Choose Minimize in the cloud instead.
Step 4: Review Your Results Quickly
Done minimizing? A pop-up will ask how you want to import results—whole trajectory, last frame, or a specific frame range. You can even center your structure around the protein or another molecule of interest.
Step 5: Visualize Convergence
In the Plots section, a graph of the system’s potential energy over the EM steps helps you quickly assess whether the minimization has properly converged.
Key values like Epot (potential energy) and Fmax (maximum force) are viewable directly in the Output window for transparent validation.
In short: For anyone setting up molecular dynamics simulations, this streamlined, visual approach to energy minimization can save hours and avoid common setup errors. It removes technical complexity while giving access to powerful customization when needed.
Want to go deeper? Explore the full Energy Minimization documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.