Running molecular dynamics simulations on large biomolecular systems can be a real challenge when your local computer lacks the necessary computational power. Crashes, long processing times, and limited storage are common issues that slow down research workflows. What if you could offload intensive simulations to the cloud—without leaving your familiar molecular design platform?
SAMSON’s GROMACS Wizard provides a streamlined approach to perform molecular dynamics steps such as NVT Equilibration, NPT Equilibration, and Production MD directly in the cloud, with minimal setup and great control over resources and costs.
When Local Isn’t Enough
Before launching a simulation in the cloud, SAMSON encourages users to try running a short local test (a few tens or hundreds of steps) to check for issues in the system. If that’s not feasible—say you’re dealing with a large protein complex—SAMSON offers an alternative: use the Generate inputs button to at least validate files before fully committing to a cloud run.
Set It Up and Choose Your Machine
When you’re ready to simulate, just click Equilibrate in the cloud or Simulate in the cloud—depending on the stage. A dialog will help you select compute resources, including:
- Machine types (CPU count, GPU presence)
- Storage size
- Estimated cost in computing credits
You can even view detailed performance metrics and pricing hints.
Confirm, Launch, and Monitor
Once you confirm your configuration, you’ll get a detailed security dialog summarizing costs and project info before launching. SAMSON’s Job manager kicks in to track job initialization and launch.
When everything is ready, a pop-up will confirm starting the simulation. You can monitor real-time job status (Initializing, Running, etc.), event messages, estimated completion time, and more.
Flexibility During Execution
One of the advantages? You’re not locked in. You can pause, restart or cancel jobs mid-simulation. Even if you close SAMSON entirely, your job continues in the background thanks to SAMSON Connect’s Cloud Service. All job information and result files are stored in your cloud workspace—even after shutdown.
After Completion: Download and Process
Once the job finishes, you’ll get a notification in SAMSON and via email. You can sort, view, and manage jobs using the Job Manager’s filtering and context menu features.
The result files can be downloaded selectively—or all at once. And there’s flexibility in how you handle these files: open them directly, show them in folders, import to SAMSON, or copy paths for use in follow-up simulations.
Clean Up When Done
SAMSON’s storage costs are very low, but it’s still best practice to delete jobs once you’re done to avoid unnecessary credit usage. The Delete action is available directly from the Job Manager.
Conclusion
Molecular modelers working with limited hardware can now seamlessly move simulations to the cloud thanks to the integrated GROMACS Wizard in SAMSON. Whether you’re testing parameters or processing a full trajectory, the workflow is intuitive and well-supported within the platform’s ecosystem.
To learn more about cloud-based simulations in SAMSON, visit the official documentation at 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.