Molecular modelers often face an important challenge: how to run computationally heavy GROMACS simulations without being limited by local hardware. SAMSON’s GROMACS Wizard offers a practical solution by enabling users to perform these simulations in the Cloud, freeing their local machines while maintaining flexibility and control over the process. This blog post outlines the advantages of using the GROMACS Wizard and provides a comprehensive guide to getting started.
Why Cloud-Based GROMACS Simulations Matter
Running simulations such as NVT Equilibration, NPT Equilibration, or Production Molecular Dynamics can be resource-intensive. Not all molecular modelers have access to powerful local hardware, and their workflows can be hindered by long computation times or system size limitations. By moving these tasks to the Cloud, you not only save time but also ensure flexibility, allowing you to carry on with lighter tasks or even turn off your local machine while the simulations run.
Getting Started with SAMSON’s Cloud Computations
First, ensure that you have at least one computing credit in your SAMSON Connect account. Credits can be checked on the SAMSON platform’s Job Manager or on your SAMSON Connect account. If needed, you can purchase additional computing credits from this page.
Setting Up Your Cloud Job
Once your input structure and simulation parameters are ready, follow these steps to launch a Cloud job:
- Generate inputs: Before committing credits, try running the job locally for a few steps or use the “Generate inputs” option to validate the setup in case of a larger system.
- Select machine type: In the GROMACS Wizard, click the “Equilibrate in the cloud” or “Simulate in the cloud” button. A machine-selection dialog will let you configure the machine based on your budget and requirements, including vCPUs, GPUs, and storage size.
- Confirm the job: A confirmation dialog will show the job details and estimated cost. You can add notes or customize the job name before continuing. Once confirmed, SAMSON initiates the job files upload to the Cloud.
Monitoring Your Simulation’s Progress
After initializing the job, SAMSON’s Job Manager becomes a central hub for tracking progress. Here’s what you can do:
- View job details: Check status updates like progress, pricing, and prediction of simulation completion time.
- Pause or cancel: Suspend ongoing simulations or restart them later as needed.
- Check events: Monitor job-specific messages and updates for troubleshooting or completion updates.
Downloading Results
When your simulation completes, you will receive a notification email and a message in SAMSON. Use the Job Manager to access the results:
- Open the job’s context menu and select “Open result window.”
- Choose the download folder and use the “Download all” button to retrieve the results. This guarantees you have all necessary files for trajectory processing or further steps. File transfers are free.
Results can be imported back into the GROMACS Wizard, where files like GRO or XT are used for visualization or advancing to the next step. 
Efficient Management of Cloud Jobs
Once you have downloaded all required results, it is recommended to delete completed jobs from the Cloud to avoid storage costs. This can be done via the Job Manager’s context menu for each job.
Conclusion
Cloud jobs in SAMSON’s GROMACS Wizard provide a streamlined, resource-efficient way to handle demanding molecular simulations. Whether you are constrained by local hardware or simply wish to multitask during simulations, the Cloud integration ensures that your work progresses smoothly and effectively.
To explore deeper capabilities or additional workflows described in the full documentation, visit https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get started today by downloading SAMSON at https://www.samson-connect.net.