Running molecular dynamics simulations can be a bottleneck in research workflows, especially when local computing resources are limited. Access to powerful hardware often means submitting jobs to institutional clusters or waiting in queues. But what if you could run GROMACS directly from your molecular modeling platform—in the cloud—with just a few clicks?
This post explores how molecular modelers can use the GROMACS Wizard within SAMSON to offload compute-intensive simulations to cloud resources. We’ll walk you through the core workflow for launching a GROMACS job in the cloud using the NVT Equilibration step as an example. The process is similar for other steps like NPT equilibration and production simulations.
Why Run GROMACS in the Cloud?
Not everyone has access to high-performance computing setups, and local machines may struggle with large systems. Running simulations in the cloud eliminates hardware limitations and offers scalability on demand. It also enables quick testing or benchmarking on different machine configurations.
Step-by-Step: Submitting a Cloud Job with GROMACS Wizard
1. Select Machine Type
After preparing your system, click the Equilibrate in the cloud / Simulate in the cloud button. A dialog box will pop up asking you to choose your machine.
You can explore various compute nodes, storage sizes, and pricing options.
2. Review and Confirm
A confirmation dialog will show the job’s configuration—name, notes, machine, and estimated cost in computing credits.
Keep in mind: though 1 credit is required to launch, the final cost may be lower.
3. Monitor Job Initialization and Status
Once submitted, the Job manager will open. It shows real-time status updates such as Starting, Running, or Completed. Click on a job to see detailed logs or status messages.
4. Post-Processing and Results
Upon job completion, you will receive a notification in SAMSON and an email. Open the Job manager again, right-click your job, and select Open result window to download results.
You can download individual files or all outputs at once. Typically, it’s a good idea to keep all files for trajectory analysis and later steps.
5. Import Results Back into SAMSON
Use GROMACS Wizard’s Import (*) results button to bring simulation output (e.g., GRO, XTC files) into your workspace for continued modeling or analysis.
Good to Know
- Jobs can be paused/resumed or canceled at any time.
- You can safely close SAMSON while the job runs; data is retrieved from the cloud later.
- Deleting completed jobs is recommended to manage storage costs, which are minimal but cumulative.
Final Thoughts
Running GROMACS in the cloud directly from SAMSON simplifies the simulation workflow for users without access to powerful local hardware. You can focus on science instead of infrastructure. Whether you’re testing setups or running production simulations, the cloud workflow gives you more flexibility and control.
Learn more about performing GROMACS computations in the cloud with SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.