One of the most common frustrations for molecular modelers running energy minimization or molecular dynamics simulations is losing control over job progress. Long computations can leave users wondering whether the job is still running, if it has completed successfully, or if an error occurred. Has the job crashed silently, or is it still processing?
This uncertainty can slow down productivity, especially when working with batches of simulations or large biomolecular systems. Fortunately, the built-in job monitoring in the GROMACS Wizard Extension for SAMSON offers a simple solution.
Real-time Job Status with the Local Jobs Button
During the Energy Minimization step, you can monitor the status of each computation thanks to the GROMACS Wizard’s job manager. Right after launching a local minimization with the Minimize locally button, a background job is created. These jobs can be tracked without interrupting your workflow — even if you’re preparing the next batch of structures.
Click the Local jobs button to open the job monitoring panel:
This will show you a list of all active and completed local jobs, along with their status. Whether you’re running a single simulation or ten batch jobs, everything stays organized in one place.
Why Use the Job Monitor?
- Parallel productivity: Run simulations in the background while working on other models in SAMSON.
- Error tracking: If a minimization job fails, you can easily spot which one and inspect its output.
- Batch management: When working with multiple systems, knowing which jobs are pending or finished helps keep experiments on track.
- Access to results: From the job list, you can launch result imports or recheck the output, plot trajectories, or rerun a step.
What Happens After Completion?
If you’ve only launched one project, a pop-up will appear offering import options as soon as the minimization finishes. If you’ve launched multiple jobs or are running batch minimizations, use the Local jobs window to manage each job’s output individually. You can then select what part of the trajectory to import — the full trajectory, the last frame, or a selected frame range — and how SAMSON should treat periodic boundary conditions.
This workflow reduces errors and unnecessary re-runs, saving both time and computational resources.
Effortless Navigation & Organization
All results are organized into folders labeled by time and job step, such as _em for Energy Minimization. This naming scheme helps identify data without having to dig through logs or rename files manually.
To learn more about managing GROMACS jobs in SAMSON, including advanced options and cloud execution, visit the full documentation on Energy Minimization in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.