Running molecular dynamics (MD) simulations can be time-consuming and compute-intensive — especially on large biomolecular systems. Molecular modelers frequently face the challenge of limited local computational resources. And while high-performance computing facilities are an option, they often involve complex setup and waiting queues.
This is where SAMSON’s GROMACS Wizard comes into play. If you’re running simulations using GROMACS, you can now launch, monitor, and analyze simulations in the Cloud — directly from your desktop — in just a few clicks.
But what exactly happens after you click “Simulate in the cloud”? This blog post walks you through the life of your Cloud job, offering insights to ensure you stay in full control, from launching all the way to results and cleanup. ⛅️🧬
1. Job Initialization
After selecting machine specs and clicking OK, SAMSON opens the Job manager where it prepares and uploads simulation files to cloud storage. Make sure to check the Running checkbox in the Job manager to view jobs in progress.
During this step, all required information such as job name, system configuration, and pricing is finalized. There’s no need to keep SAMSON open — the jobs will continue initializing independently.
2. Starting the Job
Once initialization is complete, a dialog asks you to confirm starting the job. After confirmation, you’ll see the job status change to Starting and then to Running.
You can view additional job details and messages via the Events button. This opens the full job message history, containing progress updates, error warnings (if any), and estimated time to completion.
3. Monitoring the Job
As the simulation runs, you remain in control. You can choose to:
- Pause the job
- Cancel the job
- Restart a paused job later
This flexibility can be useful if you notice an input issue, or if your modeling priorities change.
4. Completion and Retrieval
Once the job completes, you’re notified via email and a new message appears in SAMSON > Home > News.
In the Job manager, make sure to switch the job view to Non-running to find completed jobs. From here, you can:
- Analyze run performance
- Download results
- Import trajectories into GROMACS Wizard for visualization and plotting
5. Clean-Up 🚮
To avoid unnecessary charges, it’s recommended to delete the job once you’ve downloaded the results. Deleting jobs helps conserve your computing credits by freeing up cloud storage space.
You have full control over which jobs to remove. Deletion confirmation dialogs make sure there’s no accidental loss of data.
Closing Thoughts
The Cloud simulation workflow in GROMACS Wizard blends automation with human oversight. It gives you the freedom to run simulations without wrestling with server configurations or waiting lines. Whether you’re testing a system or running a production MD study, Cloud jobs let you scale your simulations easily—and safely reclaim time for analysis and insight.
To learn more about running simulations in the cloud with SAMSON’s GROMACS Wizard, see the full documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.