Running production molecular dynamics (MD) simulations can very quickly turn into a juggling act for molecular modelers: multiple files, simulation logs, and trajectories all need to be carefully tracked. If you’re running several simulations — maybe testing different parameters, different proteins, or simply repeating runs with subtle variations — it’s easy to lose track.
This blog post digs into how the GROMACS Wizard in SAMSON helps you stay organized with its local job manager feature. It’s a surprisingly underappreciated tool, especially helpful for anyone running multiple local simulations. Let’s explore how this feature can make your modeling workflow more manageable.
Why Job Management Matters
Imagine you’ve just submitted a long simulation only to realize you’ve used the wrong temperature coupling parameters. Worse, you’re unsure which input file you used. Even in small projects, this can cause real confusion.
Manually naming folders and keeping notes on every parameter variation might work in theory, but it’s fragile and error-prone in practice. This is where SAMSON’s GROMACS Wizard job manager fits in.
Meet the Local Jobs Manager
Every local simulation launched with GROMACS Wizard is managed through a built-in job manager. After launching your production MD simulation, the system runs in the background, while you can continue working in SAMSON or even set up more simulations.
To view the status of your current or past GROMACS jobs, simply click on the Local jobs button in the GROMACS Wizard panel:
This brings up a list of all your local projects. For each job, you can see its status (running, completed, failed), the launch timestamp, and useful actions like importing results or analyzing output. This lets you stay in control even when juggling multiple simulations with different input structures or parameters.
Built-in Traceability
Another helpful feature is the way results are named and organized. SAMSON automatically stores production MD outputs in folders named using the date, time, and step description — for example, a folder might end in _md to indicate a production MD run. That makes it easy to backtrack when analyzing multiple results later.
Importing and Analyzing Results
When a job finishes, if it’s the only one in the queue, a pop-up will ask if you want to import the results. If you’ve got a batch of simulations running, you can return to the job manager later to analyze a specific run. You’ll be prompted to import frames, calculate RMSD and radius of gyration plots, and choose boundary conditions.
This integrated workflow can really streamline exploratory simulations. Instead of saving dozens of notes about what you ran and when, the job manager acts as your simulation diary.
Conclusion
There’s no need to rely on guesswork, cryptic folder names, or post-it notes stuck to your monitor. With local job tracking built into GROMACS Wizard, managing your simulations becomes a lot easier — and a bit more enjoyable 🧪
To learn more, check the full documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.