Running GROMACS simulations in the Cloud can save you hardware headaches, but what actually happens once you click Simulate in the Cloud in the GROMACS Wizard? If you’ve ever wondered how your job goes from a button click to a completed simulation, this post is for you. Whether you’re running complex molecular dynamics simulations or simple equilibration steps, it’s helpful to know how the job progresses behind the scenes—and how you can interact with it at every stage.
Cloud Job Flow in SAMSON: A Quick Overview
Once your input structures and parameters are ready, and you’ve selected your machine type, clicking Simulate in the Cloud starts a series of steps. Let’s break it down.
1. Job Initialization 📁
After confirming your machine and storage choices, SAMSON prepares files and sends them to the Cloud. This setup shows up under the Job manager and is marked as Initializing.
You can click the >> button to expand job details like credits used, machine type, and current progress. This helps you catch any misconfiguration early on.
2. Starting the Job 🚀
Once files are in place, you’ll be prompted to start the job. Clicking Yes triggers the simulation, and the job status updates from Starting to Running.
You can monitor progress in the same Job Manager tab. Click the Events button to see messages from the job, including estimated completion times.
3. What if You Need to Pause? ⏸️
Jobs in progress can be paused or canceled from the context menu. Select the job, then right-click to access options. Restarting later is possible for paused jobs, which is handy for managing cloud compute time.
4. The Finish Line 🏁
When your simulation completes, you’ll receive an email and a notification inside SAMSON.
Open the Job Manager again and look under the Non-running filter to find your completed job. You’ll see the total costs (in computing credits) and detailed metadata on the job.
5. Downloading Results 💾
Double-click on the job or choose Open result window to get to the files. You can selectively download files or just hit Download all to ensure you don’t miss anything needed for later stages.
Once downloaded, these files can be imported into GROMACS Wizard for further analysis or to continue your simulation workflow.
Bonus Tip: Minimizing Storage Costs 💡
Post-download, it’s a good idea to delete jobs that are no longer required. While storage is inexpensive, it does add up. In the Job Manager, right-click a job and choose Delete. A final dialog will confirm your action.
Why Know This?
Understanding the workflow between clicking a button and getting your simulation data can help you:
- Identify bottlenecks early
- Manage credits and costs better
- Confidently pause, resume, or delete jobs as needed
Want more detail? See the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.