A molecular dynamics run can be ready to go and still run into a practical obstacle: your local machine may be too slow, or the system may be too large to run there at all. Moving a simulation to the cloud can help—but it also introduces new questions. How do you check the setup before spending credits? What happens after submission? And how do you bring the results back into your workflow?
Here’s a practical way to think about cloud jobs in GROMACS Wizard: validate what you can, understand the costs before confirming, and treat downloading and cleanup as part of the simulation workflow—not as afterthoughts.
1. Validate before you submit
Cloud computing is most useful when the simulation is ready to run, not when the setup is still uncertain. If possible, run the stage locally for a few tens or hundreds of steps first. A short test can reveal obvious problems before you commit credits to a longer job.
If the system is too large for even a short local run, choose Generate inputs instead. This can validate part of the setup and uncover common issues without requiring the full computation to run locally.
This check is especially useful for the heavier stages supported by GROMACS Wizard cloud jobs: NVT equilibration, NPT equilibration, and production molecular dynamics. Follow the local workflow for the stage you plan to run so that your structure and simulation parameters are defined first.
2. Check the estimate—not just the credit balance
Before launch, GROMACS Wizard lets you select a machine type and storage size and review their estimated costs. The machine and storage are charged; file transfer is free. Open the machine details to compare available resources and pricing. For testing, the documentation recommends the 4-vCPU machine without a GPU: it is slower, but cheaper and suitable for a test run.
There is an important distinction between the minimum balance needed to start a job and the amount that will ultimately be charged. A launch requires at least one available computing credit, but that does not mean the job costs exactly one credit. Review the expected pricing in the confirmation dialog before submitting. You can also add a useful job name, description, and notes there—small details that make it easier to identify a run later.
3. Monitor without staying glued to the job
After confirmation, the Job manager handles initialization, including preparing and copying the job files to cloud storage. Keep the Running filter enabled if you want to see jobs being initialized or running. Once initialization is complete, confirm the prompt to start the job, then check its status and event messages in the Job manager.
The event history may show an estimated finish time from GROMACS. Treat it as an estimate: it can change. You can pause a running job and restart it later, or cancel it if needed. You can also close SAMSON while a computation runs; the job remains accessible from the Job manager the next time you open the application.
4. Make results usable—and remember storage
When a job completes, check its status and event history, then open the result window from the Job manager. Download all files when possible: several may be needed to process a trajectory or import results into SAMSON. The transfer itself is free, and files left in cloud storage remain available the next time you launch SAMSON.
After downloading, copy the results-folder path and use the relevant Import (*) results button in the GROMACS Wizard stage tab. For a later stage, the resulting GRO file can also provide the input structure; the Job files window offers a command to copy its path.
Finally, plan for cleanup. Cloud storage has a cost, which may begin to be deducted from your computing credits after some time. Once you have downloaded what you need and no longer require the cloud copy, delete the job from the Job manager. Before deleting, make sure the files you need are safely downloaded.
This simple sequence—test, review the estimate, monitor, download, import, and clean up—helps keep cloud simulations manageable without losing track of either results or credits. For the full walkthrough, see the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.