Molecular dynamics simulations often take time, especially when running production-scale simulations with thousands of atoms. One common frustration among molecular modelers is that running such simulations can lock up their software or prevent them from continuing to work, forcing them to sit and wait until calculations are done.
If you’re using the GROMACS Wizard in SAMSON, there’s good news: you don’t have to pause your work while your simulation is running. Whether you’re optimizing, analyzing, or preparing the next stage of your workflow, the GROMACS Wizard’s built-in job manager helps you stay productive.
Simulate Locally Without Downtime
Once you’ve set up your molecular dynamics (MD) simulation—be it a 50,000-step test or a longer production run—you can click the Simulate locally button. The simulation will launch in the background using either the bundled GROMACS installation or a custom version you’ve specified in the settings.
While the simulation is running, you will still be able to use the SAMSON interface without interruption. That’s because the GROMACS Wizard uses a non-blocking job management system which allows the computation to continue in parallel to your interaction with the platform.
You can click the Local jobs button at any time to review the status of your active simulations. From here, you can monitor runs, view progress, and handle multiple queued simulations efficiently. This is especially useful if you are working with several systems or doing batch computations.
Flexible Output Handling
When the simulation ends, you’re not stuck with automatic behaviors. The wizard prompts you about what to do next: import the full trajectory, the last frame only, or a subset of the data, depending on what suits your analysis needs. You can also generate useful plots like RMSD or radius of gyration directly from the wizard interface.
This gives you time to quickly evaluate the results and decide if parameters need adjusting or if the simulation length was appropriate—without ever needing to restart SAMSON or lose access to your other projects.
Why It Matters
Being able to keep using your modeling environment while simulations run is not just convenient—it streamlines research. This is particularly significant for researchers and students working with limited computational resources, as it helps make better use of both machine time and human time.
Plus, with local job management, you get more control: stop, restart, monitor, and organize simulation runs without needing command-line tools or external job schedulers.
Learn more about how production simulations are handled in SAMSON and how you can monitor and manage your simulations 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.