A molecular dynamics workflow can be ready to go and still hit a practical obstacle: the next simulation stage is too demanding for the computer in front of you. Moving a run to the cloud can help, but it also raises sensible questions: How do you check the setup before spending credits? What will be charged? And how do you get the results back into your workflow?
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The useful way to approach a cloud run is not simply to press “submit,” but to treat it as a small workflow with checks before launch and file management afterward.
Run a small check before committing
If your computer can handle it, try running the stage locally for a few tens or hundreds of steps. This can reveal obvious problems before you launch a longer computation. If the system is too large to run locally, use Generate inputs instead. It validates part of the setup and may uncover common issues without requiring the full simulation to run on your machine.
Before submitting, confirm that the structure and simulation parameters are already defined, and that your SAMSON Connect account has at least one computing credit available. That one-credit threshold is a launch requirement, not a promise that the job will cost exactly one credit. The confirmation dialog displays the expected pricing for the selected job.
Choose resources for the purpose of the run
The machine-selection dialog lets you choose a machine type and storage size, and review their estimated costs. The documentation recommends a machine with four vCPUs and no GPU for tutorial testing: it is the slowest, least expensive option described, and is suitable for testing. For a real workload, inspect the available machine characteristics and pricing rather than assuming that the test configuration is the right choice.
Only machine and storage costs are charged; file transfer is free. The pricing view is especially useful before you confirm the job, when you can still review the resource choice and estimate.
Track the job without staying at your desk
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, a prompt asks you to confirm starting the job. Its status then changes from Starting to Running.
The Events view provides job messages, including an estimated finish time from GROMACS. Treat that time as an estimate: it can be updated. You can continue working in SAMSON or close it while computations run; job information is stored through the SAMSON Connect Cloud Service, and results remain in cloud storage. You can also pause a running job or cancel it from the Job manager, and restart a paused job later.
Bring back the files you will need
When the job completes, check its status and messages in the Job manager. Open the result window to access the Job files window. You can download individual files, a selection, or all files. Downloading all files is recommended because multiple files may be needed to process a trajectory or import results into SAMSON. Transfers are free, and files you have not downloaded remain available in cloud storage.
After downloading, use the file context menu to open a file, import supported formats such as GRO, XTC, TRR, or PDB into SAMSON, or copy a file or folder path. A copied path to the resulting GRO file can, for example, be used as the input structure for the next stage. To import the simulation results in GROMACS Wizard, copy the results-folder path, open the tab for the completed stage, and choose its Import results button.
Don’t forget cloud storage
Once you have downloaded what you need, consider whether the job files still need to remain in the cloud. Storage has a cost that may begin to be deducted from your computing credits after some time. The Job manager shows storage cost in the job details. Delete jobs and their files only when you are sure you no longer need the cloud copy.
This simple sequence—validate, review resources and price, monitor, download, import, and clean up—helps keep cloud computation manageable without losing track of either your data or your credits.
For the full workflow and screenshots, read the GROMACS Wizard cloud-computing tutorial.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.