If you’ve ever struggled with running computationally heavy molecular dynamics simulations on local hardware, SAMSON’s GROMACS Wizard offers an excellent solution: leveraging cloud computing to ease the burden. The process is surprisingly intuitive, and this blog post walks you through the key steps for launching, monitoring, and retrieving results from your cloud-based GROMACS simulations.
Why Use the Cloud for Molecular Dynamics?
Running simulations like NVT or NPT equilibration and production molecular dynamics often requires high-performance computing resources. However, not every molecular modeler has easy access to powerful local machines. SAMSON’s GROMACS Wizard bridges this gap by enabling you to run these processes on the cloud, providing flexibility, scalability, and performance without the upfront costs of high-end hardware. Essentially, you can “rent” the computing power only when needed, while saving time and resources during complex simulations.
Getting Started: Requirements
Before running your first job in the cloud with SAMSON, ensure you follow these preparation steps:
- Understand the Local Workflow: Familiarize yourself with the stage you want to run, such as NVT Equilibration, NPT Equilibration, or Production Molecular Dynamics.
- Ensure Credit Availability: You must have at least 1 computing credit in your SAMSON Connect account. Credits can be checked directly in SAMSON’s Job Manager or on your account page. If needed, they can be purchased easily from SAMSON Connect.
Once these steps are complete, you’re ready to set up your cloud job.
Creating and Submitting the Cloud Job
Follow these steps to launch your GROMACS simulation in the cloud:
- Check Your System (Optional but Recommended): Try running the simulation locally for a limited number of steps to verify the setup. If the system is too large for local testing, use the “Generate inputs” option to validate the structure before spending credits.
- Select a Machine: After clicking the “Equilibrate in the cloud / Simulate in the cloud” button in the Wizard, you’ll be prompted to choose the machine type, storage size, and view pricing details. For testing purposes, the machine with 4 vCPUs and no GPU is recommended, as shown below:
- Confirm Job Details: Once your machine is selected, SAMSON will display a summary of the job details, including costs. You can modify the job name, add notes, and confirm the submission.
After submission, SAMSON moves to job initialization, where input files are prepared and transferred to the cloud. This process can be monitored in the Job Manager.
Retrieving Results
When the job is complete, you’ll receive a notification by email and in SAMSON’s News section. To download results:
- Open the Job Manager and locate the completed job.
- Access the job’s context menu and choose “Open result window” to view and download available files, as shown below:
Choose the “Download all” option to ensure you retrieve the full set of output data, including crucial trajectory files for analysis.
After downloading, you can easily import the results back into GROMACS Wizard for plotting, visualizations, and further simulations. This seamless pipeline ensures that you can immediately continue your research or prepare outputs for collaboration.
Save Space: Delete Completed Jobs
Once you’ve downloaded and safely stored the results, consider deleting completed jobs from the cloud to manage storage costs (though these costs are minimal). Simply open the Job Manager, select your job, and click “Delete.”
Learn More
If you’re ready to simplify your workflow using cloud resources, visit the full documentation page at https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/ to learn more.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.