Running molecular dynamics (MD) simulations with GROMACS can be resource-intensive, particularly when working with large systems or long time scales. If you’ve ever been limited by computational power on your local machine — or had to abandon simulations partway through due to hardware constraints — this guide could make your life easier.
GROMACS Wizard in the SAMSON platform offers a straightforward way to launch MD simulations directly in the cloud. It takes just a few clicks, and you don’t need to worry about installing GROMACS or managing infrastructure.
When Should You Consider Cloud Simulations?
Cloud computing is particularly helpful in these situations:
- You’re dealing with large systems that can’t be handled locally.
- You want to free up your machine for other tasks while the simulation runs.
- You want to test different machine configurations for cost and performance tradeoffs.
Creating and Running a Cloud Job
To run simulations in the cloud using GROMACS Wizard, you’ll follow a few key steps:
1. Check Your System (Optional but Useful)
Before launching a cloud job, try running the simulation locally for a few hundred steps. This can catch system issues early. If your local machine can’t handle it, click Generate inputs inside GROMACS Wizard — this validates your setup by generating input files.
2. Choose a Machine
To start the cloud computation, click the Equilibrate in the cloud / Simulate in the cloud button. A dialog prompts you to choose machine type, storage size, and estimated cost. File transfers are free.
For testing, it’s recommended to select a machine with 4 vCPUs and no GPU, which is slower but cost-effective.
3. Confirm and Launch the Job
After selecting your machine, you’ll see a confirmation dialog with the total price and your credit balance. One credit is required to launch a job, but the actual cost may be lower.
4. Monitor Progress
The Job manager automatically opens and shows initialization progress. You can check estimated completion time in the job’s Events window.
5. Pause, Cancel, or Close
You can pause or cancel a running job if needed. Feel free to close SAMSON entirely; job status is synced via the SAMSON Connect Cloud Service and will be available when you return.
Once It’s Done…
When your job completes:
- You will receive an email notification.
- Status changes to Completed in the Job manager.
- You can download the simulation files. It’s recommended to download everything for easier processing and reproducibility.
After download, you may import the results back into GROMACS Wizard to explore trajectories, visualize data, or proceed to your next modeling step.
Cleaning Up
Cloud storage is inexpensive, but it’s best to delete jobs that you no longer need. In the Job manager, right-click a job and select Delete. This will free up your credits and clear space in your Cloud storage.
Why This Matters
Being able to run GROMACS simulations in the cloud directly from your modeling environment — without installing or managing extra software — makes this a practical solution for computational modelers. Whether you’re working on protein-ligand dynamics, materials design, or system equilibration studies, the cloud approach can speed up your workflows and make better use of your machine.
To learn more, visit the full cloud computing tutorial for GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.