A molecular simulation can be ready in the wizard but still be a poor candidate for an immediate cloud launch. Maybe a setup error will stop it, the selected machine will cost more than expected, or the results will remain in cloud storage after you have finished with them. A few checks before and after submission can help prevent wasted time and make the workflow easier to manage.
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The example below focuses on the practical decisions that apply across these stages: validate what you can, understand the cost screen, keep track of the job, and bring the results back into your project.
1. Validate the setup before spending credits
If your computer can handle it, run the stage locally for a few tens or hundreds of steps before submitting the full job. This short test can reveal obvious problems while they are still easy to address. If the system is too large to run locally, use Generate inputs instead. It does not run the simulation, but it can validate part of the setup and help uncover common issues.
This is a useful distinction: a cloud machine can provide the resources for a large calculation, but it cannot make an incorrectly prepared simulation meaningful. Check the input structure and parameters first, and consult the local workflow for the stage you plan to run.
2. Treat the machine picker as a cost decision
When you choose Equilibrate in the cloud or Simulate in the cloud, the selection dialog shows machine type, storage size, and estimated machine and storage costs. Use Open details to compare machine characteristics and pricing. For tutorial runs and initial tests, the documentation recommends the 4-vCPU machine without a GPU: it is the slowest option, but also the cheapest and suitable for testing.
Before confirming, read the security dialog’s cost summary. Cloud jobs require at least one computing credit to be available before they can start. That is a minimum balance requirement, not a statement that the job will cost exactly one credit. The actual job cost is shown in the interface; machine and storage are charged, while file transfer is free.
3. Make the job easy to identify later
Before confirming submission, give the job a clear name and, if useful, add a description or notes. This small step pays off when the Job manager contains several runs. After submission, watch the job move through initialization, starting, and running. During initialization, the files are prepared and copied to cloud storage. Check the Running filter if the job is not visible in the list.
The Job manager provides progress, events, and job details, including pricing. Event messages can show GROMACS’s estimated finish time, but the estimate may change. You can leave SAMSON open to do other work or close it; job information is stored through the SAMSON Connect Cloud Service, and you can return to the Job manager when you launch SAMSON again. A running job can also be paused or canceled, and a paused job can be restarted later.
4. Download the files you will need—not just the obvious result
When the job completes, open it in the Job manager and choose Open result window. The Job files window lets you download individual files, a selection, or everything. Downloading all files is recommended because supporting files may be needed to process a trajectory or import results into SAMSON. The transfer itself is free.
Once downloaded, use the file context menu to open a file, show it in your system’s file browser, or import compatible formats such as GRO, XTC, TRR, or PDB into SAMSON. You can also copy a file or folder path. For a multistage workflow, copying the resulting GRO file path can make it easier to use that structure as the input to the next stage.
5. Import results, then clean up cloud storage
To bring results into GROMACS Wizard, copy the results-folder path from the Job files window. Open the tab for the completed stage—for example, Equilibrate (NVT)—and select its Import results button. Paste the folder path, review the files listed for import, and confirm. Depending on the stage, SAMSON may ask how to import the trajectory or create plots.
After you have downloaded and checked the results, consider deleting the cloud job if you no longer need its files there. Storage costs are low, but the documentation notes that storage charges begin to be deducted from computing credits after some time. You can see the storage cost in the job details. Keep the cloud copy if you still need it; otherwise, delete the job from its context menu after confirming that your local results are safely downloaded.
The overall routine is simple: validate the setup, choose a machine with the cost in view, monitor the job, download the complete result set, import what you need, and remove cloud files when they are no longer useful.
For the full step-by-step workflow, see the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.