Running molecular simulations with GROMACS requires precision, but it also demands patience—especially when you’re waiting for a system to equilibrate. One of the common challenges researchers face is tracking their simulations while continuing other work. If you’ve ever found yourself hit by this bottleneck, you’re not alone.
When performing NPT equilibration in SAMSON’s GROMACS Wizard, you don’t have to sit idle waiting for results. Thanks to SAMSON’s built-in job manager, you can monitor, revisit, and manage your local GROMACS tasks without ever interrupting your modeling workflow. Let’s walk through how this helps you become more efficient in your simulations.
What Is the Local Job Manager?
The job manager is a convenient feature that becomes active once you start a GROMACS computation locally through the GROMACS Wizard Extension in SAMSON. After launching the equilibration—say the NPT step—the system adds the task to a local queue.
The magic? You can:
- See all running jobs and their status.
- Allow multiple computations to happen sequentially without manual triggering.
- Access results when the simulation completes.
- Continue to use SAMSON for other molecular modeling tasks while calculations run in the background.
Why This Matters
Let’s say you’re running an NPT equilibration, and it takes several minutes. Maybe it’s longer because you’re simulating a complex system. With conventional workflows, you’d be stuck waiting—or switching to a different tool. Not ideal.
Using the job manager, however, you just launch your calculation and continue inspecting molecules, setting up future simulations, or reviewing results from previous runs directly within SAMSON. No productivity lost.
Tracking Job Progress
Once a calculation is underway, the job manager helps you track its progress. You’ll see pop-ups updating you on current steps, warnings, or issues, if any arise. The output window gives you a real-time view of what’s happening under the hood.
And when it’s done? SAMSON brings up a prompt for result import. Whether you want to load the full trajectory, just the last frame, or a specific range, the import interface makes it easy to decide.
Recalculating Without Rework
If the system hasn’t stabilized, simply rerun the NPT equilibration using the previous results as input. Thanks to the auto-fill button, there’s no need to navigate through directories to find the right GRO file—GROMACS Wizard picks it up automatically.
Where to Find Your Results
After the job completes, the results are stored in a dedicated folder, neatly labeled by date, time, and step name (with a _npt suffix in this case). Want to reanalyze or visualize pressures and densities later? Everything is there, plotted and ready.
Conclusion
SAMSON’s GROMACS Wizard doesn’t just make simulation easier—it helps you keep simulations manageable. With a local job manager that lets you multitask and relaunch simulations without missing a step, you’re free to focus on insights rather than infrastructure.
👉 Learn more in the SAMSON documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.