A molecular dynamics run can be ready to go and still hit a practical wall: the system is too large, the simulation takes too long, or your workstation needs to stay available for other work. Moving a GROMACS stage to the cloud can help—but it also introduces new questions: how do you check the setup before spending credits, keep track of a running job, and bring the results back into your workflow?
Here’s a practical way to approach those steps with GROMACS Wizard in SAMSON. The cloud workflow supports NVT equilibration, NPT equilibration, and production molecular dynamics. The example below uses NVT, but the same job-submission pattern applies to the other supported stages.
Check before you spend
Before submitting a cloud job, make sure your SAMSON Connect account has at least one computing credit available. That is the minimum required to start a job; it is not a promise that the job will cost exactly one credit. The confirmation dialog shows the expected pricing, and the Job manager lets you inspect job details and costs.
If your computer can run the stage, try a short local run—just a few tens or hundreds of steps—to catch obvious setup problems. If the system is too large to run locally, choose Generate inputs instead. It can validate part of the setup and help reveal common issues before you launch the cloud computation.
Choose a machine for the task
Click Equilibrate in the cloud or Simulate in the cloud for the stage you have configured. The machine-selection dialog lets you choose a machine and storage size and review their estimated costs. Use Open details to compare available machines, characteristics, and pricing.
For testing, the documentation recommends the 4-vCPU machine without a GPU. It is the slowest option, but also the cheapest, making it suitable for checking the submission workflow. For a real project, compare the available machine details and the estimate with the needs of your simulation.
Only machine and storage costs are charged; file transfer is free. Before confirming, review the security dialog, which summarizes the job and expected pricing. You can also edit the job name, description, and notes—use those fields to make it easier to recognize the run later.
Monitor without babysitting
After confirmation, SAMSON prepares the job files and copies them to cloud storage. In the Job manager, enable the Running checkbox to see jobs being initialized or run. Once initialization is complete, confirm the prompt to start the job; its status should move from Starting to Running.
Use Events to view job messages and the estimated completion time. That estimate can change. You can continue working in SAMSON—or close it—and access the job later through the Job manager. If plans change while the job is running, you can pause or cancel it; a paused job can be restarted later.
Bring results back into the simulation workflow
When a job completes, you receive an email notification and a message in Home > News. In the Job manager, switch to Non-running to find completed jobs. Open the job’s result window to view its files, choose a download folder, and download individual files, a selection, or everything. Downloading all files is recommended because multiple files may be needed to process a trajectory or import results.
After downloading, copy the results-folder path from the Job files window. In GROMACS Wizard, open the tab for the completed stage and click its Import (*) results button. Choose the folder and confirm the import to load the trajectory and generate plots. You can also use a downloaded GRO file as the input structure for the next stage.
One final housekeeping step: cloud results remain in storage after download. When you no longer need them there, delete the job from the Job manager. Storage is inexpensive, but its cost can begin to be deducted from computing credits after some time.
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.