If you’re a molecular modeler working with large systems, you know the struggle: running complex simulations locally can overload your machine, lead to long computation times, or even halt your progress entirely. SAMSON’s GROMACS Wizard provides a solution to this common frustration by enabling you to offload heavy computational tasks to the Cloud.
Here’s how the process works and why it can make your modeling workflow smoother.
Why Cloud Computing for Molecular Modeling?
Heavy computational tasks like NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulations often require significant system resources. Cloud computing allows you to bypass the limitations of your local computer and access high-performance hardware without additional investment. More importantly, SAMSON’s integration makes this process easy to set up and reliable to execute.
Before You Get Started
Before diving into cloud-based computations, ensure you’ve set up your input structure and defined simulation parameters. Additionally, check that you have at least 1 computing credit in your SAMSON Connect account. You can verify this either in SAMSON’s Job Manager or from your account page on SAMSON Connect.
If you need credits, they can be purchased conveniently on the platform. For specific information, visit the Buy computing credits page.
Setting Up Cloud Jobs
Step 1: Check the System
It’s advisable to test-run the job locally for a brief period to identify any obvious configuration issues. If your machine cannot handle the system due to its size, the Generate inputs feature can help validate part of the setup before utilizing cloud credits.
Step 2: Select the Right Machine
To initiate a cloud job, click the Equilibrate in the cloud / Simulate in the cloud button for the respective task. You’ll then have the opportunity to select the machine type, storage size, and see estimated costs.
For testing purposes, SAMSON recommends selecting a machine with 4 vCPUs and no GPU, as it is both economical and effective for validation runs:
Step 3: Confirm and Monitor
Once the machine is selected, confirm the setup details in the security dialog that appears. This dialog summarizes the job specifications and estimated costs. A minimum of 1 credit is required to initiate the job, though the actual credit usage depends on the resources consumed.
After confirmation, the Job manager automatically handles job initialization and file preparation. You can track the progress in the Job manager and sort jobs by various statuses. During initialization, the files are uploaded to cloud storage seamlessly.
Step 4: Start Your Job
After initialization, a pop-up dialog will prompt you to start the job. Once started, the Job manager displays the current status as Running, and you can track progress through messages and events in the job details section.
While the computations run in the Cloud, feel free to continue other tasks in SAMSON or even close the application. The results will remain accessible through the cloud interface.
Wrapping Up
Once your simulation is completed, you’ll receive an email notification, and the Job manager will mark it as Completed. You can then download the results via the associated context menu and continue analyzing in SAMSON or your preferred software.
Cloud computing with the GROMACS Wizard is an efficient tool for molecular modelers dealing with complex systems. To explore further details, visit the official documentation page here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.