Running energy minimization jobs using GROMACS in SAMSON can be highly efficient, especially with the user-friendly interface of the GROMACS Wizard. But here’s a common challenge: how do you keep track of your jobs while continuing your work? Molecular modelers often have to juggle multiple jobs, analyze results later, or simply want to make sure everything is running smoothly without hogging system resources. Let’s take a look at how SAMSON solves this with its built-in Local jobs management system.
Why job monitoring matters
Whether you’re minimizing a single protein structure or running a batch of systems, you’ll want to know:
- Has the job finished?
- Is an error preventing the job from completing?
- Can you still work on other projects while the job runs?
- How do you import or view results later without re-running the job?
The GROMACS Wizard in SAMSON provides a clean solution—in the form of a Local Jobs manager that lets you oversee ongoing or past computations without leaving the interface.
Accessing and using the Local Jobs list
After submitting a local energy minimization job, you don’t need to keep checking a console or terminal window. Instead, click the Local jobs button, conveniently located on the GROMACS Wizard panel:
This opens the job manager, where you’ll see all your local computations, their statuses (e.g., running, completed, failed), and timestamps. From here, you can:
- Select a completed job to import results.
- Monitor progress at a glance.
- Access reports and plots once available (more on that below).
Continuing work without interruptions
One of the major conveniences this workflow provides is that you can continue working in SAMSON while your minimization job runs in the background. The GROMACS Wizard uses SAMSON’s job management engine to make sure resources are optimally allocated and system responsiveness is retained.
This is especially helpful when working on multiple systems. You can run one job while preparing the next, or analyze another structure entirely.
Importing results on your own terms
Once a job finishes, if it was the only one in the queue, you’ll get an automatic pop-up with import options. But if you were running multiple jobs or batch systems, it’s this Local jobs view that becomes your home base.
From here, you choose:
- Whether to import the full trajectory, or just the last frame.
- How to treat periodic boundary conditions.
- What to center the imported structure on (e.g., protein).
This flexibility makes job reviews feel intuitive. Any results not imported aren’t lost—they remain stored and accessible later through the jobs list or result folder.
Final tip
Each job’s result folder is named using the launch date and step—for example, energy minimization jobs end in _em. It’s an easy way to stay organized when working with multiple steps and projects.
To learn more about energy minimization and job management in SAMSON, check out the official documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/energy-minimization/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.