Running a molecular dynamics (MD) simulation is only half the story. For many molecular modelers, the real challenge comes after: importing the results, making sense of them, and preparing overview plots to check simulation health or communicate findings. If you’ve ever found yourself wondering how to efficiently bring your production MD simulation output into view within your modeling environment, this guide can help relieve that frustration.
With the GROMACS Wizard Extension in SAMSON, importing production MD results and generating basic analysis plots like RMSD and radius of gyration is a straightforward process. Here’s how it works.
Step 1: Automatic Import After the Run
Once your simulation is complete, if you ran a single simulation locally and no other jobs are waiting in the queue, a pop-up appears asking how you’d like to import the results. This includes import range options and preferences for how to treat periodic boundary conditions.
You can choose whether to import the entire trajectory, last frame only, or just a specific range. You also get options for applying periodic boundary condition (PBC) corrections and how to center the system (for example, on the protein).
Not ready for import? Simply click Cancel. The simulation’s output won’t be deleted, and you can still generate plots or analyze results later from the output directory.
Step 2: View Basic Analysis Right Away
Two pop-up dialogs follow the import prompt. The first one asks for options to generate a plot of the root-mean-square deviation (RMSD) of the structure throughout the simulation. This helps assess whether the system reaches a stable conformation and how large the fluctuations are.
The second dialog handles the plot settings for the radius of gyration (Rg). This measure provides insight into the compactness of your system, particularly when simulating proteins or macromolecules.
Together, these two simple visual reports give you immediate feedback about how your system behaved during the run and help catch common issues (like unfolding or drift).
Step 3: Access the Files Anytime
All output files are saved in the results folder, located at the top of the GROMACS Wizard interface. Folders are named using timestamps and descriptors like _md to indicate a production MD step. This makes it easy to go back, rerun analyses, or prepare snapshots or visualizations for publications or reports.
Step 4: Save and Share the Plots
Any plot generated by the Wizard can be saved simply by clicking the Save button above the figure. These plots are great for supplementary materials or for quick validation of system stability before taking a deeper dive into trajectory analysis or advanced metrics.
Summary
Importing and visualizing your simulation results doesn’t have to be difficult. By making this a built-in part of the workflow, SAMSON’s GROMACS Wizard takes care of just enough of the process to save you time — without removing flexibility or control. Whether you’re an expert or a beginner, turning raw simulation output into usable insight is now much smoother.
You can learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.