Running molecular dynamics (MD) simulations is time-consuming and often demands careful hardware usage—especially when working on a laptop or desktop that also serves other daily tasks. One of the challenges faced by molecular modelers using local GROMACS simulations is the fear of disrupting long-running computations when switching between tasks or needing to interact with the same software environment. Fortunately, if you’re using SAMSON’s GROMACS Wizard, there’s a practical feature designed to solve this: local job management.
In SAMSON, when you launch a production MD simulation using the GROMACS Wizard, calculations do not block you from using the application. Behind the scenes, a dedicated job manager handles your simulation runs, allowing you to continue working on other things, even within the SAMSON interface itself. This feature is particularly handy when you’re iteratively testing different simulation parameters or preparing the next step in your workflow.
How It Works
After triggering a local simulation with the Simulate locally button…
…the system pushes the simulation to a background process. You can then monitor the simulation status via the Local jobs button:
This opens a job manager window listing all local simulation jobs. For each entry, you’ll see essential metadata including:
- Launch time
- Step name (e.g., Production MD)
- Status (Running, Completed, Failed)
- Elapsed time
What’s the Benefit?
This may seem like a small feature, but it solves a serious user pain: not having to worry about re-launching or monitoring simulations manually. You can switch projects, prepare new batches, or even simulate other systems concurrently. For example, while one MD job is running, you could be analyzing the trajectory of the previous simulation—or even setting up another equilibration process.
This provides three main benefits to modelers:
- Efficiency: It reduces idle time between steps, since you can prepare or review other work in parallel.
- Stability: You avoid accidental interruptions by isolating long runs from the interactive interface.
- Continuity: In case something crashes or closes unexpectedly, job logs help you assess what happened.
And When It’s Done…
As soon as a simulation is complete, dialog boxes will walk you through importing results and generating common plots such as RMSD and radius of gyration:
This integration between simulation and post-processing saves time, reduces errors, and lets users reflect quickly on how their system behaved.
Conclusion
Whether you’re experimenting with new force field parameters or running multiple MD replicas, the local job manager in SAMSON’s GROMACS Wizard lets you multitask with confidence and avoid interruptions. This seemingly small feature makes a big difference when managing workflows on personal computers.
To learn more about how to run MD simulations in SAMSON with the GROMACS Wizard, visit the full tutorial here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.