Running molecular dynamics (MD) simulations using GROMACS often involves significant setup, hardware, and time. It’s not always easy for molecular modelers to configure local machines to handle large simulations, and setting up a remote compute environment can be daunting. The GROMACS Wizard in SAMSON offers a helpful alternative: launching GROMACS simulations directly in the cloud with just a few clicks.
This post walks you through the process of launching an NVT Equilibration simulation in the cloud from SAMSON, in a way that is just as simple as running it locally, but without the need for powerful hardware.
Why cloud simulations can make a difference
Whether you’re working remotely or just don’t have access to a powerful workstation, running MD simulations in the cloud can help you:
- Overcome local CPU/memory limitations
- Test systems before committing to large-scale tasks
- Switch machines without interrupting long-running jobs
- Finish simulations faster using pre-configured environments
Creating and Launching a Cloud Job
After defining the simulation parameters and preparing your system, you can launch the job with the Equilibrate in the cloud or Simulate in the cloud button. This opens a dialog where you can choose the cloud machine and storage options based on your needs and budget.
For quick tests, a 4-vCPU machine without GPU support is a low-cost starting point.
Monitoring the Job
Once you confirm the job configuration, SAMSON opens the Job manager, which gives you a detailed view of job progress, pricing, and logs. When initialization finishes, you’ll be prompted to start the job.
While your cloud job runs, you can use SAMSON for other tasks — or even close it entirely. The job continues running in the cloud and stays accessible through the Job manager the next time you restart SAMSON.
Downloading and Importing Results
Once your job is completed, you’ll receive an email and a message in SAMSON. Use the Job manager to download the result files. It’s easy to retrieve the full set of output data using the Download all button in the Job files window.
When the files are downloaded, you can import them back into the GROMACS Wizard—choose the appropriate tab for your simulation step and use the Import (*) results button. SAMSON will guide you through importing trajectories and generating plots.
Cleaning Up and Saving Credits
After retrieving your data, it’s good practice to delete completed jobs that are no longer needed. While cloud storage costs are minimal, unused data can eventually consume computing credits. Use the job’s context menu to delete it and free up storage.
Final Tips
This cloud-based workflow is especially useful when local hardware is limited or when you want a flexible environment for running, testing, and managing GROMACS simulations. With credits tracked transparently and no cost for data transfers, SAMSON provides a streamlined system tailored for research needs.
Learn more by visiting the full documentation: GROMACS Wizard – Computing in the Cloud.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.