For molecular modelers, handling computationally heavy simulations can be challenging, especially when local hardware struggles with system size or complexity. The GROMACS Wizard in SAMSON provides an elegant solution: running simulations in the Cloud. Let’s dive into how you can leverage this feature to streamline your workflow and optimize resources.
Why Run Simulations in the Cloud?
Large molecular dynamics simulations, such as NVT or NPT equilibration and production MD, can be highly resource-intensive. If you’re working on a complex model that overwhelms your local machine, using the Cloud offers the power and flexibility you need without the constant worry of system crashes or drawn-out processing times. Additionally, it allows you to free up your local machine for other tasks while the simulation progresses separately.
Prerequisites Before Cloud Launch
Before starting, ensure the following steps are complete:
- Familiarize yourself with the local workflow for your target simulation stage (e.g., NVT Equilibration, NPT Equilibration).
- Have at least one computing credit in your SAMSON Connect account. Credits allow you to access Cloud resources.
To monitor your credits, access the Job Manager in SAMSON (Interface > Job manager or use Ctrl/Cmd + 6). Alternatively, log into SAMSON Connect, navigate to your account, and check the credits there.
If needed, you can purchase additional credits directly from SAMSON Connect.
Step-by-Step Cloud Execution
1. Generate Inputs and Validate Locally
Before committing Cloud resources, consider testing the setup locally for a short duration (tens or hundreds of steps). This helps catch obvious issues early. If local testing is impractical, use the Generate inputs feature, which validates part of the setup.
2. Select Your Cloud Machine
To launch a Cloud job, click the Equilibrate in the Cloud / Simulate in the Cloud button for the selected stage. The machine-selection dialog lets you choose the machine type, storage size, and estimated costs. For testing or tutorial purposes, we recommend the 4 vCPUs machine without a GPU, as it is cost-effective.
For advanced users, clicking Open details provides a breakdown of machine specifications and pricing.
3. Confirm and Initialize the Job
After selecting your machine, confirm the job details in the summary dialog. Here, you can modify the job name, description, and notes before submission. Once submitted, the Job Manager will automatically open, and SAMSON will prepare the necessary files for the Cloud.
Make sure the Running checkbox in the Job Manager is enabled to track initialization progress.
4. Start and Monitor the Job
Once initialization is complete, start the job by confirming in the pop-up dialog. The job status will change from Initializing to Running, and progress updates will be visible in the Job Manager.
Check the Events section in the Job Manager to view messages and the estimated completion time.
5. Download Results
Once the job is complete, you’ll receive a notification via email and the Home > News section in SAMSON. Use the Job Manager to access completed jobs, download results, and import them back into GROMACS Wizard for analysis.
Downloading all files is recommended, as many may be required for trajectory processing or visualization. You can import the results directly into GROMACS Wizard to proceed with the next stages of your workflow.
Get Started Today
Transitioning resource-demanding simulations to the Cloud with SAMSON’s GROMACS Wizard is simple and efficient. Learn all the details on how to make the most of this feature by visiting the full documentation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get started by downloading SAMSON at https://www.samson-connect.net.