After running molecular dynamics simulations, especially in tools like the GROMACS Wizard in SAMSON, a common question arises: What exactly should I import from my simulation? This may seem like a simple decision, but it can impact your analysis workflow significantly — especially when working with larger systems where memory and time are limited.
In this post, we’ll look into the choices offered by the GROMACS Wizard after completing an NVT (constant Number of particles, Volume, and Temperature) equilibration run, and help you understand which import scenario might work best depending on your situation.
Why Import Options Matter
When the equilibration finishes, you’re prompted to choose how much of the resulting data to import into your project. If you’re running multiple jobs — say, as part of a batch — you may prefer to skip this or fine-tune how much data you load to avoid slowing down your system.
You can choose to import:
- The full trajectory – useful if you’re planning additional analysis to assess equilibrium behavior over time (e.g., temperature plots, RMSD, etc.).
- Only the last frame – optimal for stepping forward to the next stage (such as NPT equilibration) with minimal memory use.
- A specific range of frames – handy if you’re interested in a particular time window, such as a period of instability or rapid change.
Periodic Boundary Conditions and Centering
Another key choice available upon import is whether and how to deal with Periodic Boundary Conditions (PBCs). This is essential for ensuring molecules that wrap around the simulation box appear as a single entity. If not treated correctly, molecules might look split across the box boundaries.
You can also select what part of your system you want to center in the visualization — for instance, centering on the protein backbone is a common practice when working with protein-solvent systems.
Visual Feedback to Guide You
Not sure whether equilibration was successful? The GROMACS Wizard automatically produces a temperature-over-time plot so you can confirm that the desired value has been stably reached.
If the system’s temperature hasn’t stabilized, you may choose to re-run the NVT step using the output from the first trial as input. This can be done quickly with the auto-fill option, which will suggest the correct file automatically.
What If You Cancel?
If you’re not sure what to do with the results just yet, you can safely click Cancel on the import pop-up. This won’t delete anything — the files are saved and a trajectory plot is still generated. You can import the results later, once you’ve decided on your next steps.
Choosing Wisely
Here are some quick guidelines:
- For large systems: Importing only the last frame saves resources.
- For troubleshooting equilibration: Import the full trajectory and analyze temperature evolution.
- For progressing to the next simulation step: Last frame may be all you need.
GROMACS Wizard makes these choices simple, yet it’s worth understanding the implications so you stay in control of your workflow.
To learn more about NVT equilibration and result handling in SAMSON, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.