Running molecular dynamics (MD) simulations can be computationally intensive, especially for large systems. This often limits researchers to what their local hardware can handle, or forces them to navigate complex HPC systems. If you’re a molecular modeler looking for a simpler solution, the GROMACS Wizard in SAMSON offers built-in cloud capabilities that might make your life easier.
Let’s explore how to painlessly run MD simulations in the cloud using GROMACS Wizard, including selecting resources, monitoring jobs, and retrieving results.
Why Cloud Computing for MD Simulations?
Setting up simulation environments and managing hardware can be time-consuming. The GROMACS Wizard in SAMSON allows you to launch cloud-based simulations in a few clicks, without system administration hassles, and with transparent cost control based on computing credits.
Getting Started: Choose Your Cloud Resources
After specifying equilibrated systems and simulation parameters (steps like NVT, NPT, or production MD), you can launch the job in the cloud by clicking Equilibrate in the cloud or Simulate in the cloud.
A dialog offers machine type, storage size, and associated costs. For testing, you can choose a small CPU-only machine (e.g., 4 vCPUs) to conserve credits. Click OK to proceed.
Confirm and Launch
A confirmation dialog will summarize job details and associated costs. You can also rename the job, add a description, or notes. You’ll need at least 1 computing credit to launch a job, although the actual cost might be less.
Track Job Progress
Once launched, use the Job manager in SAMSON (shortcut: Ctrl/Cmd + 6) to monitor your simulation.
Status will transition from Starting to Running. Click Events to monitor system messages and see the expected completion time.
Job Completion and Result Retrieval
When a job finishes, you’ll receive a SAMSON notification and an email.
From the completed job’s context menu, access the Job files window to download results.
It’s best to download all files using Download all—essential for trajectory analysis and re-import into GROMACS Wizard. File transfer is free, and files remain accessible in the cloud until deleted.
Importing Results Back in SAMSON
Click Import (*) results in the relevant tab inside GROMACS Wizard (e.g., NVT Equilibration). Paste the path to your downloaded folder to auto-detect result files.
The Wizard will load your data and provide analysis options like trajectory visualization and plots, streamlining the workflow from simulation to insight.
For full instructions, performance recommendations, and detailed visuals, check out the official documentation: GROMACS Wizard: Computing in the Cloud.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.