Running a molecular dynamics (MD) simulation is a critical step in exploring the dynamic behavior of molecular systems like proteins, membranes, or drug candidates. But once the simulation ends, the next challenge can feel just as important — making sense of the results. If you’ve ever asked yourself, “Now what?” after a simulation finishes, this post is for you.
This guide walks through the result analysis component of the GROMACS Wizard in SAMSON, focusing on the post-simulation import and visualization features in the Production MD step. Whether you ran your MD calculation locally or in the cloud, knowing how to deal with the output effectively can save you time and help you make informed scientific decisions.
Importing Results Made Simple
After the simulation is complete, SAMSON intelligently asks how you’d like to process the results. If only a single project is running, a pop-up dialog helps you select the best import options. For batch jobs or multiple simulations, use Local jobs to monitor completion status and import results.
You’ll get clear prompts to customize how your data is managed:
- Choose your frames: Import the entire trajectory, just the last frame, or a specific range.
- PBC Treatment: Apply periodic boundary condition corrections automatically.
- System Centering: Set the reference point — for example, center your result on the protein.
Not ready to load the trajectory? You can opt-out without losing your data or visualizations. The system still generates plots for quick insight.
Understanding Your Simulation with Auto-Generated Plots
Two key plots are automatically created to help interpret your simulation:
- RMSD (Root Mean Square Deviation): This shows how the structure evolves over time, compared to its initial configuration. If your RMSD stabilizes, you may conclude that your system reached equilibrium.
- Radius of Gyration: Useful for checking structural compaction and stability. Drastic changes suggest unfolding or large conformational shifts.
If your simulation included pulling (e.g., an umbrella sampling setup), you’d also see pull force and coordinate plots, providing a window into external manipulations imposed on the system.
All plot data is saved in your results folder, which is automatically named based on launch time and labeled with _md for easy identification. You can save plots manually with the Save button embedded in the plot window.
Why This Matters
Too often, researchers complete simulations but delay or overlook analysis due to time constraints, unclear tools, or unintuitive workflows. SAMSON’s GROMACS Wizard simplifies this step, offering structured dialogs and instant plots that reduce confusion and highlight trends in your molecular system.
Efficient result import and interpretation helps ensure you don’t miss important system behavior that can influence your next steps. Getting clarity on structural drift or conformational stability is more than academic — it’s foundational to drug discovery, materials design, and molecular engineering.
To learn more, visit the full tutorial page: Production Molecular Dynamics Simulation in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.