Molecular modelers often face a common challenge: managing computationally intensive simulations on local machines. This not only slows down workflows but can also overwhelm system resources, especially for large models. The GROMACS Wizard in SAMSON offers an intuitive solution by allowing users to perform molecular dynamics computations directly in the cloud. Here’s how you can streamline your simulations while preserving your local resources.
Why Use the Cloud for GROMACS Simulations?
Running simulations locally can be limiting when dealing with complex systems or extended simulations requiring significant computational power. The GROMACS Wizard in SAMSON now lets you harness cloud computing for key tasks such as NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation. With just a few clicks, you can offload demanding computations to the cloud, freeing up your local resources while ensuring accurate results.
Prerequisites for Cloud Computation
Before launching a simulation in the cloud, ensure you have your input structure and parameters ready. This guide assumes that groundwork has been completed. Additionally, you need at least one computing credit in your SAMSON Connect account. You can check your available credits by either:
- Using the Job Manager within SAMSON (via
Ctrl/Cmd+6) and clicking the Show credits button. - Logging into SAMSON Connect and accessing the “My account” section.
If you need additional computing credits, you can conveniently purchase them at Buy computing credits.
Key Steps to Start Cloud Computation
1. Select the Machine and Resources
From the GROMACS Wizard, click the “Equilibrate in the cloud” or “Simulate in the cloud” button, depending on your simulation step. A dialog will pop up to help you select the type of machine and resources required. For tutorials and testing, a machine with 4 vCPUs and no GPU is recommended as it is cost-efficient.
2. Confirm the Job
After selecting the machine, you’ll be prompted to confirm the job. This dialog displays job details, costs, and your available credits. Note that even though at least 1 credit is required, the actual cost might be lower depending on the duration and machine specifications.
3. Initialization and Monitoring
Your job will initially go through an automatic initialization phase where input files are prepared and uploaded to cloud storage. Open the Job Manager (via Ctrl / Cmd + 6) to monitor the status. Once initialized, you’ll be prompted to confirm starting the job. As the computation runs, you can use the SAMSON interface or even close it while the job executes in the cloud.
Fetching Results
After the simulation completes, a notification will be sent to your registered email, as well as in SAMSON under Home > News. Use the Job Manager to download the results. Click “Open result window” in the job’s context menu to access the files.
It’s advisable to download all files for compatibility with trajectory analysis or follow-up steps. The download process is free of charge, ensuring cost efficiency. Once download is complete, you can import the results directly into GROMACS Wizard for visualization and further processing.
Effortless Cloud Integration
Utilizing the GROMACS Wizard for cloud-based simulations offers molecular modelers a practical and resource-saving approach, especially for highly demanding calculations. By following these steps, you can complete simulations efficiently while making the most of SAMSON’s intuitive interface and its integration with cloud services.
To explore further capabilities, visit the full documentation at https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON now at https://www.samson-connect.net.