A molecular dynamics workflow can be ready to go and still hit a familiar obstacle: the system is too large, or the next simulation stage is too demanding for your local machine. Moving a job to the cloud can help, but it also raises practical questions: How do you avoid spending credits on a setup mistake? How do you keep track of a job after submission? And how do you get the results back into your analysis workflow?
GROMACS Wizard in SAMSON supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The key is to treat cloud computing as a managed workflow—not just a remote “Run” button.
Validate before you spend
Before launching a cloud job, try running the stage locally for a few tens or hundreds of steps. A short test can reveal obvious problems before you commit resources. If the system is too large to run locally, use Generate inputs instead. This can validate part of the setup and expose common issues without requiring a full local simulation.
Also check that your SAMSON Connect account has at least one computing credit available. That is the minimum balance required to start a cloud job—not necessarily the amount the job will cost. You can check your balance in the SAMSON Job manager using Show credits, or in My account on SAMSON Connect.
Choose a machine with the estimate in view
When you select Equilibrate in the cloud or Simulate in the cloud, the machine-selection dialog lets you choose the machine type and storage size and review estimated costs. Use Open details to compare available machines and their characteristics. For a first test, the tutorial recommends the 4-vCPU machine with no GPU: it is the slowest option, but also the cheapest and suitable for testing.
Only machine and storage costs are charged; file transfer is free. Review the pricing shown for your selected resources, then check the security confirmation dialog before submitting. It summarizes the job and its expected pricing, and lets you edit the job name, description, and notes. A clear name and a short note about the system or simulation stage can make later job lists easier to interpret.
Monitor the job, even if you leave
After confirmation, SAMSON prepares the job files and transfers them to cloud storage. In the Job manager, enable the Running checkbox to see jobs that are initializing or running. Once initialization is complete, confirm the start when prompted; the status should move from Starting to Running.
The Events view contains job messages, including an estimated completion time from GROMACS. Treat that time as an estimate: it may be updated. You can continue working in SAMSON or close it while the computation runs. Job information is stored through the SAMSON Connect Cloud Service, and results remain in cloud storage for later access. A running job can also be paused or canceled from its context menu; paused jobs can be restarted later.
Bring back the complete result set
When the job is complete, you receive an email notification and a message in Home > News in SAMSON. In the Job manager, select Non-running to find completed jobs. Open the job’s result window to see its files and choose a download folder.
For most workflows, downloading all files is the safest choice: multiple files may be needed to process the trajectory or import results into SAMSON. Transfer is free, and files you have not downloaded remain available in cloud storage. After downloading, use the job’s Copy button to copy the results-folder path. In the matching GROMACS Wizard stage, choose Import (*) results, paste the folder path, and confirm the import. Depending on the stage, you may be asked about plotting or trajectory-import options.
Close the loop on storage
Once you have downloaded and imported what you need, decide whether to keep the cloud copy. Storage is inexpensive, but its cost can start being deducted from your credits after some time. Check the storage cost in the job details, and delete jobs you no longer need from the Job manager. Make sure you have downloaded the files you want to keep before deleting the job.
This simple sequence—validate, estimate, monitor, download, import, and clean up—helps make cloud computing a practical extension of a local GROMACS workflow.
Learn more in the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.