Running molecular dynamics simulations in the cloud can save you time and free up your local resources—but what happens if your input files are misconfigured or your system isn’t stable enough? In SAMSON’s GROMACS Wizard, you have a handy option to check your molecular system before launching simulations in the cloud, and it’s a simple step that could help you avoid wasted credits and debugging headaches.
This blog post walks you through an approach that helps reduce risk before cloud execution—by pre-validating your system locally or generating input files to verify compatibility.
Why Pre-Check Your System?
Cloud simulations in SAMSON rely on computing credits. If your system fails midway due to setup issues, your credits might still be consumed. This is frustrating, especially when simulations are aborted before any meaningful results are produced.
To prevent this, GROMACS Wizard offers a useful option to check your system locally or to generate input files, even if you cannot run the job fully on your local machine.
Two Ways to Validate
Before diving into cloud simulations, here are your two go-to methods:
- Run a short test locally. If your machine can handle smaller simulations and you are unsure about the system stability, run just a few tens or hundreds of steps locally. This is often enough to surface configuration issues like incorrect topologies or missing files.
- Use the “Generate inputs” button. Even if your system’s size prevents running local simulations, this option will generate the input files and perform a preliminary validation. It’s a lightweight way to catch structural or formatting issues before actual submission.
Here’s a quick highlight from the documentation:
Note: Even though this image is about choosing a cloud machine for testing, it’s an example of choosing safer, lower-cost options for pre-checks.
When Should You Do This?
- You’re modeling a new system for the first time.
- You’ve made significant changes to molecular topology or parameters.
- You’ve manually edited input files outside SAMSON.
- You want to be cautious before spending computing credits.
Bonus Tip: Use the Cheapest Machine for Test Runs
If you’re still inclined to try a trial simulation in the cloud, use the test machine with 4 vCPUs and no GPU. It’s slower but more economical and perfect for short validations. Here’s what it looks like:
Conclusion
Pre-checking your system before launching cloud jobs establishes a good habit that saves both time and cloud credits. Whether you’re a beginner or a seasoned molecular modeler using GROMACS Wizard, taking this small step can help streamline your computation pipeline.
Want more details on how this fits in the bigger workflow? View the full cloud simulation guide for GROMACS Wizard at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.