Launching molecular dynamics simulations can be time-consuming and demanding on local machines, especially when working with large systems or when you want to stay productive while simulations run. Fortunately, if you’re using SAMSON, there’s a streamlined way to run GROMACS simulations in the cloud using the GROMACS Wizard.
This blog post breaks down the essentials of creating and launching a cloud-based GROMACS job in SAMSON. If you’ve struggled with managing local resources or waited hours (or days) for simulations to complete, this method might help you.
When should you use the cloud?
While running simulations locally can be faster for quick tests or small systems, the cloud becomes essential when:
- Your local machine doesn’t have enough RAM, CPU, or GPU resources.
- You want to keep working during long simulations.
- You’re managing multiple simulations in parallel.
Setting up your cloud job in SAMSON
Once you’ve prepared the system and simulation parameters using the GROMACS Wizard, follow these steps to set up a cloud job:
- Choose ‘Simulate in the Cloud’ in the GROMACS Wizard. You’ll be prompted to select a machine type.
- Select a machine based on your needs. For testing, a machine with 4 vCPUs and no GPU is the most cost-effective choice. You’ll also be able to see pricing per machine.
- Review and confirm the job. A dialog shows job details and your available computing credits. Confirm to submit the job to the cloud.
- Monitor initialization in the Job Manager. SAMSON prepares the job and uploads it to the cloud. You can track progress, view events, and more from the Job Manager.
Starting and monitoring your job
You’ll be prompted to start your job once initialization completes. After confirming, the job status moves from Starting to Running, and SAMSON will provide an estimated time of completion based on GROMACS’ internal estimate.
You can keep working or even close SAMSON — job tracking and management are handled by the SAMSON Connect Cloud Service. You can always reopen the Job manager on your next session to monitor or retrieve results.
What happens when a job finishes?
SAMSON notifies you via email and through the News tab once the job completes. In the Job Manager, sort by completed jobs using the Non-running checkbox and review your job cost and results.
Downloading and importing your results
From the Job Manager, access Job Files to download your simulation outputs. You can download individual files or everything at once — file transfers are free of charge.
Once downloaded, importing results into GROMACS Wizard is simple. Navigate to the corresponding simulation step (e.g., NVT Equilibration), click Import (*) results, select the downloaded folder, and confirm to load trajectories and generate plots.
Tips for staying organized
- Use file-specific context menu tools to quickly open directories or copy paths.
- Tag your jobs with notes and custom descriptions to keep track of test conditions.
- Delete jobs you no longer need to minimize cloud storage costs.
Running your GROMACS simulations in the cloud through SAMSON provides flexibility and efficient resource management, especially when you’re balancing multiple projects or dealing with large biomolecular systems.
To explore this feature in more detail, view the full documentation at SAMSON Docs: GROMACS Wizard – Cloud Computing.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.