A molecular dynamics run can turn a productive workday into a waiting game: your workstation is busy, a large system may be difficult to test locally, and you still need to know whether the job completed successfully and where its results went. GROMACS Wizard’s cloud workflow offers another option for NVT equilibration, NPT equilibration, and production simulations. The key is to treat it as a complete process—not just a button that starts a remote run.
Here’s a practical way to avoid common surprises, keep track of costs, and bring the results back into your project.
1. Check the setup before spending credits
Start by defining the input structure and simulation parameters for the stage you plan to run. When practical, run a short local test—just a few tens or hundreds of steps—to catch obvious setup problems before launching a cloud job. If your computer cannot run the system locally because it is too large, use Generate inputs to validate part of the setup and look for common issues.
Also check your SAMSON Connect computing credits before submitting. You can view them from the Job manager in SAMSON using Interface > Job manager, or the Ctrl/Cmd + 6 shortcut, then click Show credits. You can also check your account on SAMSON Connect. At least one credit must be available to start a cloud job; that is a minimum to launch, not a promise that the job will cost exactly one credit.
2. Choose a machine with the test in mind
The machine-selection dialog lets you choose a machine type and storage size and review their estimated costs. Open the machine details to compare available resources, performance hints, and pricing. For tutorial runs and testing, the documentation recommends a 4-vCPU machine without a GPU: it is slower, but cheaper and suitable for testing.
Before confirming, read the security dialog. It summarizes job details and expected pricing, and lets you edit the job name, description, and notes. A descriptive name can make it easier to identify the run later in the Job manager.
3. Follow the job through its changing states
After submission, SAMSON prepares the job files and copies them to cloud storage. In the Job manager, enable the Running checkbox to see jobs that are initializing or running. When initialization finishes, a dialog asks you to confirm that the job should start. Its status then changes from Starting to Running.
Use the Events button to inspect job messages. The event history can show an estimated completion time from GROMACS, but that estimate may change. While the job runs, you can work elsewhere in SAMSON or close the application; the job information is stored by the SAMSON Connect Cloud Service, and results remain in cloud storage. Jobs can also be paused or canceled from the job list, and paused jobs can be restarted later.
4. Download the complete result set
When a job completes, SAMSON sends an email notification and a message appears in Home > News. In the Job manager, switch to Non-running to find completed or canceled jobs. Open a completed job by double-clicking it or choosing Open result window from its context menu.
In the Job files window, choose a download folder. You can 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 into SAMSON. File transfer is free; machine and storage costs are what are charged.
Once downloaded, the context menu offers useful ways to work with files: open a text log in your operating system’s associated viewer, import supported formats such as GRO, XTC, TRR, or PDB into SAMSON, or copy a file or folder path. A resulting GRO file path, for example, can be used as the input structure for a later step.
5. Import results, then tidy up cloud storage
To bring results into GROMACS Wizard, copy the results-folder path in the Job files window. Go to the tab for the corresponding stage—such as Equilibrate (NVT)—and click its Import (*) results button. Paste the folder path into the dialog and confirm the import. Depending on the stage, SAMSON may ask how to plot data or import the trajectory.
After confirming that you have downloaded what you need, consider deleting the cloud job if you no longer need its files there. Storage costs are low, but they can begin to be deducted from computing credits after some time. The Job manager shows storage cost in the job details. Deleting is therefore a useful final step in keeping track of both your results and remaining credits.
A simple checklist: validate the setup, check credits and estimated pricing, monitor job events, download all needed files, import the results, and remove cloud files you no longer need.
For the full walkthrough and screenshots, learn more in the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.