A molecular dynamics setup can be ready to run and still be too large for your workstation. That creates a familiar dilemma: start a long calculation and hope your machine keeps up, or postpone the simulation until you have access to more computing power. GROMACS Wizard offers another option: submit supported equilibration and production stages to cloud hardware, then return to your work while the job runs.
The key to using cloud computing efficiently is not just knowing where to click. It is checking the setup before spending credits, understanding what the estimate covers, and making a plan for retrieving and cleaning up the results. This workflow applies to NVT equilibration, NPT equilibration, and production molecular dynamics; the examples here use NVT.
Check the setup before using cloud resources
Before submitting a job, make sure the input structure and simulation parameters are defined. If your computer can manage it, run the stage locally for a few tens or hundreds of steps. A short test can reveal obvious setup issues before you commit to a cloud run.
If the system is too large to run locally, use Generate inputs instead. This can validate part of the setup and help catch common problems without requiring you to run the simulation on your machine. It is a useful middle ground: you can check what is feasible before choosing cloud resources.
Choose a machine with the cost in mind
Click Equilibrate in the cloud or Simulate in the cloud for the stage you want to run. In the machine-selection dialog, review the machine type, storage size, and estimated costs. Use Open details to compare the available machines, their characteristics, and pricing.
For testing, the tutorial recommends a machine with 4 vCPUs and no GPU. It is the slowest option, but also the cheapest, making it suitable for checking the submission workflow. That does not mean it is the right choice for every production calculation: use the machine details and estimate to select resources appropriate to your work.
Only machine and storage costs are charged; transferring files is free. Before submitting, confirm the expected pricing in the security dialog. You need at least one computing credit available to start a cloud job, but that minimum is not the amount the job will necessarily cost. The dialog also lets you edit the job name, description, and notes, which can make it easier to identify the calculation later.
Track the job without staying at your desk
After confirmation, SAMSON opens the Job manager and initializes the job by preparing and copying its files to cloud storage. Check the Running filter to see jobs being initialized or run. Once initialization is complete, confirm the start when prompted. The job status changes from Starting to Running.
Use the job’s Events button to read messages and see the estimated completion time. Treat this as an estimate: the time may be updated. You can pause a running job or cancel it from its context menu; a paused job can be restarted later. You can also continue using SAMSON or close it. Job information is stored through the SAMSON Connect Cloud Service, and results remain in cloud storage until you retrieve or delete them.
Download results in a way that supports the next step
When the job completes, SAMSON sends an email notification and adds a message under Home > News. In the Job manager, switch to the Non-running filter to find completed jobs. You can inspect the status, events, and computing-credit cost there.
Open the completed job’s result window to access its files. Choose a download folder, then download individual files, a selection, or all files. Downloading all results is recommended because multiple files may be needed to process a trajectory or import results into SAMSON. File transfer is free.
After downloading, use the Copy button to copy the results-folder path. In the relevant GROMACS Wizard tab, click the corresponding Import (*) results button, paste the folder path, and confirm the files to import. Depending on the simulation stage, you may be prompted for trajectory-import or plotting options. You can also copy the path to a resulting GRO file and use it as the input structure for the next step.
Remember cloud storage cleanup
Downloaded files remain available in cloud storage. When you no longer need the job or its cloud files, delete the job from its context menu in the Job manager. Storage costs are low, but they can begin to be deducted from computing credits after some time. Check the storage cost in the job details, and make sure you have downloaded the files you need before deleting the job.
This sequence—validate what you can, compare the estimate, monitor the run, download the needed files, and clean up cloud storage—helps make an otherwise hardware-limited simulation easier to manage. For the full walkthrough and screenshots, see the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.