When running molecular dynamics (MD) simulations, especially those that take time to compute, a common frustration among molecular modelers is not being able to track progress easily without interrupting their workflow. Whether you’re testing new force field parameters, prepping simulations for publication, or batch-processing large systems, staying informed about what’s going on in the background is crucial.
Fortunately, SAMSON’s GROMACS Wizard offers a simple yet powerful way to handle this: a built-in job manager that keeps your simulations visible and under control without getting in your way. If you’re the kind of modeler who prefers visual feedback over command-line guessing — or you just want to keep things moving — this feature is for you. 👇
Where to Find the Local Job Manager
Once you’ve launched a Production MD simulation locally, a background job is started. This doesn’t block your interface, and you can continue setting up other simulations, analyzing molecules, or preparing inputs. But where do you check on the current simulation?
Head over to the Local jobs button in the Simulate tab of the GROMACS Wizard:
Clicking this button brings up a panel showing all running and previous GROMACS jobs initiated within the GROMACS Wizard. You can track:
- Status (running, completed, failed)
- Job names with timestamps
- Progress percentage (if applicable)
- Access paths to result folders
Why This Matters
❓ Tried running multiple simulations but forgot which ones you already launched?
📈 Wondering whether that last simulation finished or crashed silently?
💾 Need to retrieve previous results or clean up job folders?
Instead of deep-diving into directories or scrolling through logs, the job manager provides a centralized dashboard to manage your local MD workflow.
Paired with Real-Time Feedback
During the simulation, output is shown in a separate output window. If any issues arise (missing parameters, trajectory problems, etc.), they appear there. But the local job manager sticks around after that window is closed — helping you remain in control over time.
No Setup Needed
The local job manager works out-of-the-box once you start local simulations. There’s no need to configure additional logging or job schedulers. This consistency is a real time-saver, especially if you’re juggling simulations on limited hardware and want quick access to information.
Bonus: Results Tied to Jobs
Every production job creates a results folder, including RMSD and gyration radius plots, and your simulation trajectory. The job manager helps you map each job to its corresponding output. Folders are automatically named with the launch date and simulation step, such as:
|
1 |
2024-05-04_17-20-33_md |
No more guessing which folder belongs to which project.
In Summary
Monitoring MD simulations doesn’t need to be a blind process. With the GROMACS Wizard in SAMSON, local simulation management is clear, reliable, and integrated. The local job manager helps you:
- Track ongoing GROMACS simulations without interruption
- Access result folders directly from the interface
- Keep a history of completed tasks
Explore this practical tool and streamline your simulation workflow today. Learn more in the full tutorial section.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.