Molecular modeling can be a meticulous process, and when a production molecular dynamics (MD) simulation wraps up, there’s often a big question: What did it produce, and how do I interpret it?
The GROMACS Wizard in SAMSON makes life a little easier—but as with all simulations, there’s value in knowing what’s under the hood. If you’ve reached the end of an MD run using the GROMACS Wizard and are now staring at new folders, progress bars, and pop-ups, this post is here to guide you through the results.
What to Expect When the Simulation Ends
Once your MD simulation completes, the GROMACS Wizard prompts you with a few options for importing and analyzing the results. This includes whether you want to import the entire trajectory, just the final frame, or a specific frame range. You can also decide how to handle periodic boundary conditions (PBCs) and what to center your system on—for instance, the protein structure.
This level of flexibility is helpful, especially if you’re working on large systems or planning downstream analysis like clustering or principal component analysis (PCA). Importantly, even if you choose not to import the trajectory, you’ll still be able to generate summary plots.
Quick Visualization: Plots That Matter
After import, the software automatically generates two plots: a Root Mean Square Deviation (RMSD) plot and a Radius of Gyration (Rgyr) plot. These are more than just nice graphs—they’re essential tools for assessing the stability and compactness of your structure during the simulation.
The RMSD plot gives you insight into how your structure evolves over time compared to the initial conformation. A plateau often suggests structural stability. The radius of gyration provides a measure of compactness. If both plots stabilize over time, that’s typically a sign that your system has equilibrated well.
Additional plots for pulling simulations, like umbrella sampling, are also automatically generated, showcasing pull force and coordinate evolution. It’s a small detail, but extremely helpful if you’re running more advanced techniques.
Where Are the Results Stored?
GROMACS Wizard names result folders using a timestamp and the step description. For instance, after a production MD simulation, the folder suffix will be _md. You can find the path to these results at the top of the GROMACS Wizard interface in SAMSON.
If you ever need to go back and retrieve plots or trajectories, this is where they live. Plots can be saved manually by clicking the Save button on each figure.
Managing Multiple Jobs
If you’ve launched several jobs, the Local jobs interface becomes especially useful. Here, you can keep an eye on different job states and re-import results manually if necessary. You’ll also appreciate that job management doesn’t stall your workflow—you can continue using SAMSON while simulations run in the background.
Plot Customization and Reuse
Once plots are generated, you can reopen them later, customize their view, or even export them for presentations or lab reports. It’s a streamlined way to go from simulation to analysis with fewer manual steps.
Understanding your results isn’t just about knowing what buttons to click—it’s about knowing what the outputs mean. GROMACS Wizard bridges that gap by combining sensible defaults with enough user control to dig deeper.
To explore this in more detail, visit the original documentation page on Production Molecular Dynamics in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.