Running molecular dynamics simulations can often feel like juggling. You launch one equilibration job… then another… and before you know it, you’re wondering what has finished, what is still running, and where the results were saved.
If you’re using the GROMACS Wizard in SAMSON, you’re already saving time setting up your systems. But did you know that it also comes with a built-in job manager designed to help you track and manage your simulations?
This article guides you through how to monitor GROMACS simulation jobs locally using the GROMACS Wizard’s job management interface–a particularly helpful feature when working on multiple NVT or NPT equilibrations or batch computations.
Launching Simulations and Staying Informed
After you click Equilibrate locally to start your NVT run, a window will pop up showing job progress. But what if you need to check back later? Or you’ve launched multiple jobs at once?
This is where the Local Jobs button comes in. Located conveniently within the GROMACS Wizard interface, it opens a summary of all local jobs you’ve dispatched using the wizard.
What Can You See In the Job List?
- Status of each job — whether it’s queued, running, completed, or failed.
— useful when tracking which particular phase each job belongs to (e.g., energy minimization, NVT, or NPT). — including links to the generated folders where input/output files and plots are stored.
This not only saves you from searching your directory structures for output folders but also keeps your workflow organized.
Managing Multi-Step Workflows
If you’re following a standard simulation workflow—minimization → NVT → NPT → production—each step generates new input files for the next. The job manager helps you keep track of these transitions. For example, after completing an NVT equilibration, you’ll want to continue to the NPT step using the final configuration from the NVT phase. The status view in Local Jobs helps you identify which job just finished, making it easier to auto-fill paths or select the right GRO file for the next step.
Batch Jobs? Even More Useful
Batch computations can get complex, especially when you submit tens or hundreds of simulations at once. Each one might finish at a different time. The local job manager keeps everything in view, prompts you to import results, and reduces the chance you miss a job that quietly finished hours ago.
Final Tip: Results Are Not Lost
If for any reason you skip importing results when prompted (e.g., you click Cancel), data is still saved. Just revisit the result folder listed at the top of the GROMACS Wizard interface, where folders are named using the time/date and step, such as 2024-04-12_15-45-23_nvt.
So next time you’re launching multiple molecular dynamics jobs, know that SAMSON’s GROMACS Wizard is keeping an eye on them for you.
To learn more about using SAMSON for NVT equilibration, check out the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.