One of the persistent challenges in computational molecular modeling is maintaining productivity while long tasks — like energy minimization — are running. If you’ve ever initiated a simulation and found yourself waiting, uncertain whether to keep SAMSON running or not, you’re not alone. Fortunately, the GROMACS Wizard in SAMSON offers a solution that helps you stay productive: background job management.
When you launch an Energy Minimization in SAMSON via the GROMACS Wizard, you don’t have to sit idle. The minimization process can run in the background, thanks to the integrated job manager of the GROMACS Wizard Extension. A small but powerful UI detail — the Local jobs button — gives you direct access to all currently running or finished tasks.
What Exactly Happens in the Background?
Once you click the Minimize locally button, GROMACS launches the computations using either the built-in or a user-defined version of GROMACS. The simulation begins, but SAMSON stays responsive. This allows you to:
- Explore different parts of your project
- Set up new simulations
- Post-process other results
The active minimization is tracked quietly through the GROMACS Wizard job manager. If you initiated multiple jobs (or a batch minimization), they’re all listed and monitored here.
Why This Matters
Job management may sound like a small feature, but it solves several real problems:
- Uncertainty: Was the job successful? Is it still running? Should I wait? The job list gives you clear visibility.
- Multitasking: You can work on different aspects of your project without freezing or duplicating sessions.
- Resource control: If you realize something went wrong or needs adjustment, you can manage or stop jobs efficiently.
Pro Tips
💡 When the computation finishes, a pop-up will appear allowing you to control how results are imported:
- Import the last frame only or the whole trajectory
- Apply a specific Periodic Boundary Condition (PBC) treatment
- Center the molecule on your protein or solvent
And If You Cancel the Import?
It’s good to know that canceled imports don’t delete your results — everything is stored in the results folder named according to the launch time and task (e.g., ending in _em for energy minimization).
This approach also scales: batch jobs each get their own subfolders, outputs, and minimization plots. You can check those plots for the behavior of potential energy over time, helping you assess convergence before moving further in your simulation workflow.
Conclusion
If you’re spending time modeling molecular systems with SAMSON, remember you don’t need to stop working each time a simulation runs. Let the GROMACS Wizard manage your local jobs in the background, and make the most out of every minute.
To learn more about the energy minimization workflow in GROMACS Wizard, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.