A molecular simulation can be ready to run and still hit a practical limit: the system is too large for your workstation, or you need to keep your local machine available for other work. Moving a GROMACS calculation to the cloud can help—but it also raises sensible questions. How do you check the setup before spending credits? How do you follow the job? And how do you make sure the results are safely back on your computer?
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The key is to treat the cloud run as a managed workflow: validate what you can, review the cost before confirming, monitor the job, and download the files you will need for the next step.
Check the setup before committing resources
Before launching a cloud job, make sure your input structure and simulation parameters are defined. If possible, run the stage locally for a few tens or hundreds of steps. This short test can reveal obvious setup problems before you use cloud computing credits. If the system is too large to run locally, choose Generate inputs instead. It can still validate part of the setup and help uncover common issues.
You’ll need at least one computing credit available to start a cloud job. That is a minimum requirement, not a promise that the job will cost one credit. Review the expected pricing in the machine-selection and confirmation dialogs before submitting. The charge covers machine and storage costs; file transfers are free.
Choose a machine for the task
The machine-selection dialog lets you choose the machine type and storage size, and see estimated costs. Open the machine details to compare available resources, characteristics, and pricing. For a tutorial or initial test, the documentation recommends a machine with 4 vCPUs and no GPU: it is the slowest option, but also the cheapest and suitable for testing.
Once you select a machine, the security dialog summarizes the job, including expected pricing and the credits currently available. You can also edit the job name and description or add notes. Use those fields to make the run easy to identify later—for example, by recording the simulation stage or a short project label—then confirm only when the details look right.
Monitor progress without staying at your desk
After confirmation, SAMSON opens the Job manager and initializes the job. Check the Running filter to see jobs being initialized or run. When initialization is complete, a prompt asks you to confirm starting the job. Its status should then move from Starting to Running.
The Events button opens the job message history, where you can check updates and the estimated completion time. Treat that time as an estimate: it can change. You can pause a running job or cancel it from its context menu, and restart a paused job later. You can also close SAMSON while a job runs; the job information is stored by the SAMSON Connect Cloud Service and can be accessed from the Job manager when you open SAMSON again.
Bring back the files you’ll need
When the job is complete, you’ll receive an email notification and a message in Home > News. In the Job manager, switch to the Non-running filter if you don’t see the completed job. Open its result window to view the files and choose a download folder.
Although you can download individual files or a selection, downloading all files is recommended: several may be needed to process the trajectory or import the results into SAMSON. Transfers are free. After downloading, you can import compatible files such as GRO, XTC, TRR, and PDB through their context menus, or copy the results-folder path and use the relevant Import (*) results button in GROMACS Wizard.
One final housekeeping step can prevent unnecessary storage charges: after you have downloaded what you need, delete jobs whose cloud files you no longer need. Storage is inexpensive, but its cost can begin to be deducted from your computing credits after some time. Check the storage cost in the job details before deciding what to keep.
This workflow helps separate two concerns: cloud computing can handle a demanding stage, while downloaded results let you continue analysis and the next simulation step locally. 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.