Energy minimization is a critical step in preparing molecular systems for simulations, ensuring that your model is stable and ready for further refinement. But for many molecular modelers, especially those working with personal computers, a common problem arises: How do you run minimizations effectively without losing access to your software, and how can you monitor these jobs efficiently?
The GROMACS Wizard in SAMSON addresses this seamlessly with built-in job management tools that let you run simulations locally, monitor them in real-time, and continue working without interruptions. Here’s an overview of how to make the most of it.
Why Run Minimization Locally?
Running minimization on your local machine is cost-free and immediate. If you’re working on small to moderately sized systems and want quick feedback or don’t want to rely on cloud credits, this is often the best route.
Once your structure is prepared, switch to the Minimize tab in the GROMACS Wizard. Here, you’ll find a user-friendly interface for loading input files, setting parameters, and, importantly, launching the job locally:
Launching and Tracking Jobs with Ease
Clicking the Minimize locally button launches your energy minimization job directly on your computer. To monitor your active jobs, the GROMACS Wizard offers a Local jobs manager:
This interface lets you:
- Track the progress of all currently running jobs
- Access results of completed jobs
- Handle multiple jobs simultaneously
All of this happens without blocking your session—so you remain free to create, visualize, and even prepare the next steps in your workflow.
Importing and Interpreting Results
After the job completes, the system prompts you to import results. You can choose to import the full trajectory, a single frame, or a specific frame range. Applying periodic boundary conditions and choosing the system’s center (e.g., the protein) are also available options.
If you’re importing only select data (like the final structure), just click “Last frame” and import. You’ll still have access to all simulation outputs stored in the job’s result folder.
Check Convergence at a Glance
Don’t forget the plots. GROMACS Wizard automatically creates a graph of potential energy (Epot) over minimization steps. This visual helps verify that the energy decreases steadily—a good sign of convergence.
Look for a downward trend, and check that the final potential energy is negative and stable. For further confidence, check the output log for the maximum force (Fmax) and compare it against your target tolerance (default: emtol = 1000.0).
Flexible, User-Friendly, Efficient
With an intuitive local job manager, automated result import, and visual feedback, SAMSON’s GROMACS Wizard makes minimizing molecular systems not just simpler, but more seamless—especially for scientists working with limited local resources or small research teams.
To explore all the features in detail, including launching jobs in the cloud and applying custom parameters, visit the full documentation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.