Launching molecular dynamics simulations can be resource-intensive, particularly for large systems. If you’ve ever struggled with local hardware limitations when using GROMACS, you’re not alone. A common frustration among molecular modelers is the inability to test a system before committing significant computing resources — especially in the cloud, where jobs sometimes fail due to solvable issues in the input structure.
Fortunately, SAMSON’s GROMACS Wizard offers a helpful workflow to minimize the chances of failure: a way to check your system before launching cloud-based calculations. This small but powerful step can save time, computing credits, and avoid delays in your simulation pipeline.
Why Check First?
It’s easy to get excited and jump straight to production simulations — but doing so without first verifying your setup can lead to frustrating failures. One of the most reliable practices is to run a short local test (dozens to hundreds of simulation steps) before sending a job to the cloud.
This initial dry-run can reveal:
- Missing or misformatted input files
- Topology or parameter inconsistencies
- Numerical instabilities due to system setup
Testing locally is especially recommended when working with a new or modified system. And if you can’t run it locally due to hardware limitations? There’s still a way: use GROMACS Wizard’s “Generate inputs” functionality. This pre-validates the job by creating and examining the necessary simulation files, highlighting issues without launching the full computation.
How to Perform a Pre-check
- Set up your system in SAMSON, defining structures and simulation parameters for your intended NVT, NPT, or production run.
- Instead of clicking the Equilibrate in the Cloud or Simulate in the Cloud button, try a short local run (a few tens or hundreds of steps).
- If your machine cannot handle local runs, click “Generate inputs” in the GROMACS Wizard — this checks your files and prepares the simulation package.
Although optional, this step is highly recommended. Pre-checking ensures your cloud job won’t fail due to input errors — and lets you use your computing credits more efficiently.
Additional Tips
- Use the cheapest available machine (e.g., the 4 vCPU without GPU option) for initial testing in the cloud.
- Preview storage and compute costs in the machine selection dialog before launching the job.
- Label your jobs clearly using the name and notes fields during job creation — it helps maintain clarity when managing multiple simulations.
The job checking process fits seamlessly into the existing GROMACS Wizard workflow. Once you’re confident in your system, moving forward to the cloud is just a click away.
Taking a couple of minutes for a quick validation now can save you hours of troubleshooting later. SAMSON’s tools are designed to make this process as intuitive as possible.
Want to explore other steps like starting, monitoring, or downloading results from a cloud-computed GROMACS job? You can learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.