A molecular simulation can be ready in principle but still be a poor candidate for a cloud run: perhaps the system is too large for your workstation, the setup contains an error, or you are unsure what the run will cost. A little preparation can reduce wasted compute time and make the results easier to retrieve and reuse.
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The same basic workflow applies to each stage. Here is a practical way to approach it, from preflight checks to cleanup.
1. Validate what you can before spending credits
First, make sure the input structure and simulation parameters are defined, and read the local workflow for the stage you plan to run. If your computer can handle it, try a short local run—tens or hundreds of steps—to catch obvious setup problems. This is a useful preflight, not a substitute for the full simulation.
If the system is too large to run locally, use Generate inputs instead. It validates part of the setup and may reveal common issues before you submit a cloud job. That distinction matters: you can check some of the preparation without needing your computer to complete the simulation.
2. Treat the machine choice as a trade-off
Before launching, check that your SAMSON Connect account has at least one computing credit. The credit balance is available from Show credits in SAMSON’s Job manager, or on the My account page of SAMSON Connect. The launch dialog also shows remaining credits and expected pricing.
That one-credit requirement is a minimum to start a job; it does not mean the job costs exactly one credit. Machine and storage costs are charged, while file transfer is free. Open the machine details to compare available resources and pricing before choosing. For tutorial runs and testing, the documentation recommends a 4-vCPU machine without a GPU: it is the slowest option, but also the cheapest and suitable for testing.
Once you select a machine, review the security confirmation dialog. In addition to pricing, you can set the job name and description and add notes. A descriptive name can make it easier to identify the run later in the Job manager.
3. Monitor the job—and know what the estimates mean
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. When initialization is complete, a prompt asks whether to start the job. Its status should move from Starting to Running.
Use Events to read job messages, including the estimated completion time. That time comes from GROMACS and can change, so treat it as an estimate rather than a fixed deadline. You can continue working in SAMSON or close it; job information is stored through the SAMSON Connect Cloud Service, and results remain in cloud storage. A running job can also be paused or canceled, and a paused job can be restarted later.
4. Download for the next step, then remove what you no longer need
When the job is complete, open it from the Job manager and use the Job files window to download results. Downloading all files is recommended because multiple files may be needed to process a trajectory or import results. Transfers are free. Once downloaded, files can be opened, imported into SAMSON, or used to copy a file path—for example, to set a resulting GRO file as the input structure for the next stage.
To bring results into GROMACS Wizard, copy the results-folder path, open the tab for the completed stage, and click its Import (*) results button. Select the folder and confirm the import. Depending on the stage, GROMACS Wizard may offer plotting or trajectory-import options.
Finally, consider cloud storage as part of the job’s cost. Results remain available in the cloud until you delete the job, and storage charges may begin after some time. Check the storage cost in the job details; once you have downloaded what you need, delete jobs you no longer need to keep in the cloud.
This workflow helps you catch setup issues early, make a deliberate resource choice, and keep completed results ready for the next simulation step. 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.