Running molecular dynamics simulations—especially in the cloud—can consume both time and computational credits. For researchers using SAMSON’s GROMACS Wizard, launching a simulation in the cloud is surprisingly easy. However, when something goes wrong during a run, troubleshooting can be frustrating and costly.
That’s why SAMSON provides a simple but effective recommendation before submitting jobs to the cloud: test your setup locally first. In this post, we’ll explain how a quick local trial run can help you catch problems early and avoid wasting cloud credits.
Why testing locally matters 🧪
Imagine setting up an NVT or NPT equilibration step, uploading to the cloud, waiting several minutes… only to have your job fail due to a minor configuration error, a missing file, or a poorly prepared input structure. The impact is not just lost time—it also means used-up computing credits.
Local testing lets you quickly verify that your system is configured correctly before you commit cloud resources. Even running a simulation for just a few hundred steps is usually enough to surface the most common issues.
How to run a local check
If your machine is capable of running a GROMACS simulation, simply select an appropriate step (like NVT Equilibration) and try launching it locally. If you’re working with a large structure and your computer cannot handle the local run, there’s another fallback option built into the GROMACS Wizard: the Generate inputs function.
This feature not only prepares the input files needed for the simulation, but also performs basic validation checks. You won’t be running the simulation yet, but it will warn you about potential configuration errors or missing elements that could derail a cloud run.
What if your system is too large for local runs?
In those cases, generating input files is still a good strategy. Even without running the full simulation, you’ll know whether the job is technically viable. This kind of early feedback can help you adjust parameters or correct file paths before committing to the cloud infrastructure.
Benefits of local validation
- ✅ Spot issues with topology and parameters early
- 💸 Avoid wasting computing credits
- ⏱️ Shorten debugging cycles for complex systems
Where to find these options in SAMSON
You will find both the Run locally and Generate inputs options in the interface for each simulation step. While local runs may take a few minutes, they’re a sound investment that could save hours and resources in the long run.
Conclusion
Using SAMSON’s GROMACS Wizard to run MD simulations in the cloud is convenient, but taking a moment to test your setup locally acts as a safeguard. It’s a small step that can have a big impact on the efficiency of your workflow.
To learn more about cloud simulations in SAMSON, visit the full tutorial documentation: https://documentation.samson-connect.net/tutorials/gromacs-wizard/cloud/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.