A molecular simulation can be ready to run long before your workstation is. Larger systems and longer production runs can make local computing impractical, but moving a job to the cloud raises its own questions: What will it cost? How do you know the setup is ready? And where do the results go when the run finishes?
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. A useful way to approach the process is to treat it as a series of checkpoints: validate the setup, understand the estimate, monitor the job, and bring the results back before cleaning up stored files.
Validate before spending credits
Before submitting a cloud job, make sure the input structure and simulation parameters are defined. If your machine can handle it, try running a short local segment—just a few tens or hundreds of steps—to catch obvious setup problems. If the system is too large to run locally, use Generate inputs instead. It can validate part of the setup and help reveal common issues before you launch the full computation.
Cloud jobs require at least one computing credit available to start. That is a minimum balance requirement, not a promise that the job will cost exactly one credit. Check your balance in SAMSON’s Job manager using Show credits, or sign in to SAMSON Connect and check My account.
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 their estimated costs. Machine and storage are charged; file transfer is free. Open Open details to compare available machines, their characteristics, and pricing.
For testing, the tutorial recommends a machine with 4 vCPUs and no GPU: it is slower, but cheaper and suitable for checking the process. Once you are comfortable with the setup and workflow, you can choose a machine based on the needs of your actual simulation. Before confirming, review the security dialog’s job details and expected pricing. You can also edit the job name and description and add notes, which can make it easier to identify the run later.
Monitor progress without babysitting the run
After confirmation, SAMSON prepares the job files and copies them to cloud storage. In the Job manager, enable the Running checkbox to show jobs being initialized or run. When initialization is complete, confirm the prompt to start the job. Its status should move from Starting to Running.
Use the Events button to read job messages, including an estimated finish time. Treat that time as an estimate: it may be updated. You can pause or cancel a running job from its context menu, and restart a paused job later. You can also close SAMSON while computations run; job information is stored with the SAMSON Connect Cloud Service, and you can access jobs through the Job manager when you launch SAMSON again.
Retrieve results—and remember storage
When the job completes, you’ll 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 access its files. Choose a download folder, then use Download all. Downloading all files is recommended because several may be needed to process a trajectory or import results into SAMSON. Transfers are free.
After downloading, use the folder path in GROMACS Wizard’s relevant stage tab and click Import (*) results. The wizard can import the results and create plots; the available options depend on whether the job was an equilibration or production simulation. For a subsequent stage, the path to a resulting GRO file can also be copied and used as the next step’s input structure.
One final housekeeping step matters: results remain in cloud storage until you delete the job. Storage costs are low, but can begin to be deducted from computing credits after some time. Once you have downloaded what you need and no longer need the cloud copy, delete the job from its context menu in the Job manager.
This workflow helps separate the decisions that are easy to overlook: check the setup before launch, review the estimate before confirmation, download the files needed for analysis, and remove cloud data when you are done with it.
For the complete walkthrough and screenshots, see the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.