Running molecular dynamics (MD) simulations is only half the work—the other half is interpreting and importing your results correctly. Many molecular modelers face the recurring challenge of efficiently handling large MD simulation data, especially with regards to choosing what to import, what to visualize, and how to ensure it’s aligned with goals like structural validation or analysis tracking.
If you’re using the GROMACS Wizard in SAMSON, the good news is that importing and visualizing results post-simulation is already streamlined. But to make the most of it and avoid clutter or unnecessary computing overhead, here are some tips and insights that can make your workflow cleaner and more efficient.
What happens after the production MD run?
As soon as your simulation completes—whether it was a quick local job or a larger cloud-based production—you’ll be prompted with options to import the results. These dialogs are more powerful than they might appear at first glance.
The first dialog allows you to configure how the Root-Mean-Square Deviation (RMSD) plot is generated. You’ll be comparing the current trajectory to a reference structure. This is crucial for tracking system stability or conformational changes over time.
Immediately after, you’ll get similar options for the radius of gyration plot—helpful for assessing the compactness or structural unfolding of your model throughout the simulation.
Making selective choices
The third dialog box you’ll encounter might be the most essential: it lets you choose how much of your simulation trajectory you want to import. Maybe you don’t need all 50,000 frames—just the final structure, or a specific range of interest.
Here are some options you should pay attention to:
- Import only key frames: Useful when you’re only looking for endpoints or a representative structure.
- Periodic Boundary Condition (PBC) treatment: This adjusts how the protein or molecule appears spatially. Choose the right scheme if you’re planning further visualization or analysis.
- Centering the system: Often, centering on your protein or solute simplifies downstream visualizations.
Can’t decide on the spot? Click Cancel. Your simulation data remains safe, and the plots will still be generated and available for inspection.
The Result Folder: Your Digital Filing Cabinet
Every production MD run is saved in a timestamped folder with the _md suffix inside the Results Folder set in the GROMACS Wizard. This ensures all your simulations are organized chronologically and contextually. You can revisit them anytime for re-import or extended analysis.
And here’s a helpful tip: if you’ve run a batch of jobs, the Local jobs section gives you a quick overview of job status and which ones are ready for import.
Why import smartly?
Efficient importing means faster turnaround on data processing, less clutter in your workspace, and less time waiting for unnecessary file loading. This can significantly improve your productivity, especially when handling large or numerous projects.
To learn more about running and analyzing production MD simulations using GROMACS Wizard, visit the full documentation at this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.