Running molecular dynamics (MD) simulations with GROMACS can be computationally heavy, especially when preparing longer trajectories or simulating large biomolecular systems. Local hardware often becomes a bottleneck — not everyone has access to clusters or high-end GPUs, and even test runs can slow down your workflow.
Fortunately, SAMSON’s GROMACS Wizard offers a simple alternative: running GROMACS simulations directly in the cloud, without leaving your working environment. Whether you’re performing NVT/NPT equilibration or full production runs, offloading to the cloud can free up your system and speed up results – all with just a few clicks. Here’s how it works.
What You Need First
Before launching jobs in the cloud, make sure you:
- Have already set up your system and simulation parameters (covered in local setup tutorials).
- Have at least 1 computing credit in your SAMSON Connect account.
You can check credits via the Job manager in SAMSON (Interface > Job manager or Ctrl/Cmd + 6), or via the “My account” section of SAMSON Connect.
Choosing Your Machine
Click the Equilibrate in the cloud or Simulate in the cloud button (depending on what step you’re running). You’ll be prompted to choose machine specs and storage size. Selecting a machine with no GPU and 4 vCPUs is great for initial tests, as it’s affordable and reliable.
Click OK to proceed, then confirm the job details, including cost and credits available.
Monitoring Progress
Once submitted, your job is automatically initialized and uploaded. The Job manager keeps track of status (initializing, starting, running). You can safely close SAMSON; the job continues in the cloud.
When the first results are available, you’ll be notified inside SAMSON and by email. You can monitor completion estimates, inspect events, and check progress details.
Downloading and Using Results
After the simulation completes, open the Job manager and use the context menu to download all results.
Once downloaded, you can:
- Import the trajectory directly into GROMACS Wizard.
- View logs or structures in your OS’s default viewer.
- Copy the file path to feed results into follow-up steps — extremely useful for iterating through NVT → NPT → production runs.
Why Offload to the Cloud?
This workflow is especially valuable when:
- Your local hardware can’t handle moderately sized systems.
- You want to keep working on other projects while simulations run.
- You need to run test cases without clogging your workstation.
The cost is predictable (shown before launching), and file transfers are free. You only pay for compute and storage — and if you don’t need the results in the cloud anymore, delete the job to avoid storage deductions in your credit balance.
To learn more and follow the full step-by-step instructions, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.