Running molecular dynamics (MD) simulations can be computationally intensive, especially when dealing with large systems. For many researchers, these heavy computational requirements can slow down project workflows and strain local hardware. What if there was a way to offload these computations while maintaining flexibility and control? Enter GROMACS Wizard’s cloud computing feature in the SAMSON platform.
This guide focuses on how you can optimize your workflow by using GROMACS Wizard to submit, monitor, and retrieve calculations performed on cloud-based hardware. Whether you’re setting up NVT/NPT equilibration or production molecular dynamics stages, the cloud option offers an efficient alternative.
When Should You Use Cloud Jobs?
Cloud resources can make a significant difference for tasks that are too heavy to run on local machines. Before submitting a job to the cloud, it’s wise to check your setup on your local machine for a few tens or hundreds of steps. This helps identify obvious issues without spending precious cloud computing credits. If your system is too large for local testing, simply choose the ‘Generate inputs’ option in the GROMACS Wizard to partially validate the setup.
Step-by-Step Guide to Performing GROMACS Stages in the Cloud
1. Preparing Your Environment
Before launching your first cloud job, ensure your SAMSON Connect account has at least 1 computing credit. You can check your credit balance directly in SAMSON by opening the Job manager (Interface > Job manager or via shortcut Ctrl/Cmd + 6). Alternatively, log in to your SAMSON Connect account and check under “My account.” If credits are needed, you can purchase them on the SAMSON Connect website.
2. Submitting a Cloud Job
To begin, define your input structure and simulation parameters. From GROMACS Wizard, navigate to the specific stage (e.g., NVT Equilibration) and click the “Equilibrate in the cloud / Simulate in the cloud” button. This opens the machine-selection dialog, where you can choose:
- The type of machine (e.g., number of CPUs or GPUs).
- The required storage size.
- The estimated cost for machine time and storage.
For testing purposes, a machine with 4 vCPUs and no GPU is often recommended for its cost-effectiveness. Select your machine, confirm job details in the security dialog, and proceed.
3. Monitoring Cloud Jobs
Once submitted, the Job manager will track your job’s progress in real time. During initialization, files are uploaded to Cloud storage, and the job transitions from ‘Starting’ to ‘Running.’ You can review detailed progress and event histories directly in the interface. These logs also provide an estimated completion time, though it may adjust periodically. Pro tip: While your job runs, you can continue working or even close SAMSON—your job data is safely stored in the Cloud.
4. Retrieving Results
When the job is finished, you will receive notifications via email and within SAMSON. In the Job manager, locate the completed job. From its context menu, open the Job files window to download results to your local machine. You can selectively download or quickly retrieve all files depending on your needs. Importing these results back into GROMACS Wizard lets you proceed to subsequent stages seamlessly.
Why Use Cloud Resources?
Cloud computing offers more than just extra muscle—it allows flexibility. You can design simulations locally while scaling jobs to match computational demands without expensive hardware investments. Plus, SAMSON ensures a smooth interface between your data and cloud workflows.
Learn More
For more detailed instructions, visit the full documentation at GROMACS Wizard Cloud Jobs. Here, you’ll find additional tips on using custom GROMACS parameters and related tutorials for maximizing your productivity.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.