A molecular dynamics setup can be ready long before your workstation is ready to run it. Large systems and longer simulations may take substantial local resources, while sending a job to the cloud without checking the inputs first can waste both time and computing credits. A useful middle ground is to validate what you can locally, submit only the demanding stage to cloud hardware, and plan how you’ll retrieve and clean up the results.
GROMACS Wizard supports cloud jobs for NVT equilibration, NPT equilibration, and production molecular dynamics. The process is similar for each stage. The example images below show NVT, but the same general submission and result-handling pattern applies to the other supported steps.
Validate before you spend
Before choosing a machine, make sure the input structure and simulation parameters are defined. If your computer can handle it, run the stage locally for a few tens or hundreds of steps. This short test can expose obvious setup problems before you commit to a cloud run. If the system is too large to run locally, use Generate inputs instead; it can still validate part of the setup and reveal common issues.
This small check is especially useful when a run has multiple stages. Catching an input problem before a longer cloud job is easier than discovering it after waiting for a job to finish.
Choose resources with the purpose of the run in mind
When you click Equilibrate in the cloud or Simulate in the cloud, the machine-selection dialog lets you choose a machine type and storage size, and shows estimated machine and storage costs. File transfer is free; machine and storage costs are charged. Use Open details to compare available machines, their characteristics, and pricing.
For a tutorial or an initial test, the documentation recommends the 4-vCPU machine without a GPU. It is the slowest option, but also the cheapest, and is suitable for testing. For a production run, compare the available options rather than assuming the smallest machine is always the best fit: the right choice depends on the job and the balance you want between cost and performance.
Understand the credit confirmation
Before submitting, check your computing credits in the Job manager using Show credits, or sign in to SAMSON Connect and look under My account. The launch confirmation summarizes the job and expected pricing, and also shows your remaining credits. A job needs at least one credit available to start; that is a minimum requirement, not a statement that the job will cost exactly one credit. Review the estimate shown in the dialog before confirming.
You can also edit the job name and description and add notes. Clear names and notes are practical when several equilibration or production jobs are active: they help you recognize which system or stage a job belongs to later.
Keep track of the job, even if you close SAMSON
After confirmation, 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. Once initialization finishes, a dialog asks you to confirm the start. The status then changes from Starting to Running.
Use the job’s Events button to inspect messages, including the estimated completion time. That estimate comes from GROMACS and may be updated, so treat it as a guide rather than a fixed deadline. You can continue working in SAMSON or close it; the job information is stored by the SAMSON Connect Cloud Service, and results remain in cloud storage. You can reopen the Job manager the next time you launch SAMSON.
Download, import, and tidy up
When a job is complete, check the Non-running jobs in the Job manager and confirm its status and messages. Open the result window to access the Job files. Choose a download folder, then download individual files, a selection, or all files. Downloading all files is recommended because additional files may be needed to process a trajectory or import results into SAMSON. Transfers are free.
After downloading, use Copy in the Job files window to copy the results-folder path. In the corresponding GROMACS Wizard stage, choose Import (*) results and paste that path. The wizard can then display the files to import and, depending on the stage, offer trajectory and plotting options. The resulting GRO file’s path can also be copied and used as the input structure for a following step.
Finally, once you have downloaded everything you need, consider deleting the cloud job and its files. Storage is inexpensive, but its cost may begin to be deducted from your computing credits after some time. Check the storage cost in the job details and keep cloud files only as long as they are useful to your workflow.
For the complete walkthrough, see the GROMACS Wizard cloud-computing documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.