One common challenge for molecular modelers working with GROMACS is dealing with long-running energy minimization calculations. These simulations can temporarily block workflow, especially when computational resources are limited. Fortunately, the SAMSON GROMACS Wizard has integrated local job management capabilities that can help you multitask more effectively and stay organized.
When you launch an energy minimization task in SAMSON using the GROMACS Wizard, you don’t have to pause your entire modeling session. Behind the scenes, the Wizard offloads computations to a local job manager. This means simulations run in parallel, without hijacking your interface—so you can continue designing molecules, setting up other simulations, or reviewing past results while the job runs.
This is particularly helpful for iterative projects or when testing system sensitivity to various minimization settings.
How the Local Job Manager Works
After you click the Minimize locally button, your job is submitted to the local queue. You’ll still see occasional pop-up messages about progress, but these won’t lock your interface.
To monitor the status of all running jobs, simply click the Local jobs button. This opens a panel showing the state of each job—whether it’s queued, running, or completed. If you’ve launched a sequence of batch jobs, each subproject is displayed individually, making it easier to track multiple systems.
Importing Results When Ready
Once a job finishes, you are prompted to import its results. You can choose to import the entire trajectory, only the last frame, or a range of frames. You can also apply periodic boundary corrections and set centering preferences. For instance, you might want to center your system on the protein backbone to better visualize solvation effects.
If you’re not ready to import the data just yet, you can simply hit Cancel. This won’t discard the results, and plots will still be available in the output folder named after the run timestamp and suffixed with _em for energy minimization jobs.
Why It Matters
For researchers managing multiple simulations, this job management system reduces friction in your workflow. There’s no need to keep track of output files manually or switch between terminal windows and interfaces. SAMSON’s local job manager provides a single hub to monitor simulations and retrieve data when you’re ready.
In summary, integrated job control in the SAMSON GROMACS Wizard gives molecular modelers more freedom and efficiency, especially when working on complex projects or large systems.
To learn more about how the GROMACS Wizard handles energy minimization jobs, visit the original documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/energy-minimization/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.