If you’ve spent time preparing a molecular dynamics system for simulation, you’ve probably run into this scenario before: you’re ready to move to the next step, but you can’t remember where your last output file was saved—or what it was named. You start browsing folders, checking timestamps, and wondering if that confout.gro was from the last successful minimization run or an older test.
This kind of friction might seem minor, but it slows down your workflow and adds mental overhead to simulation preparation. For molecular modelers juggling multiple simulation steps or running batch projects, this small task becomes repetitive and error-prone.
Fortunately, the GROMACS Wizard in SAMSON offers a straightforward solution during the NVT equilibration step: automatic input detection.
Simplifying input selection: the auto-fill feature
After minimizing your system, the next step is generally to perform an NVT equilibration to stabilize the temperature. This step requires input—either as a .gro file from the previous phase or a SAMSON batch project.
Rather than manually finding and inserting the path to these files, SAMSON offers an auto-fill button:
Located next to the input field, this small button checks your previous actions and fills in the correct input path, automatically detecting whether you used a single project file or a batch mode result from earlier. This is especially useful when you’re following a sequential workflow—such as moving from energy minimization to NVT equilibration—as it eliminates guesswork and reduces the chance of accidentally using the wrong configuration file.
Manual fallback remains
If you do want finer control or need to pull input from a different file entirely, the option to manually choose a .gro file remains available through the … button. This way, you benefit from convenience while maintaining flexibility.
Batch project compatibility
The auto-fill feature isn’t limited to single-file projects. If you’re running simulations in batch mode—a common scenario for parameter sweeps or high-throughput molecular design—you can still benefit from automatic input path detection.
Whether your input is batch or single-project based, the system intelligently references your last successful minimization or equilibration step as the new starting point. This enables smoother pipelines and supports reproducibility by reducing manual input errors.
Why this matters
In molecular dynamics, reproducibility and accurate simulation flows are key. Every manual step—especially those involving file paths—is a potential place for human error. When tools support automatic continuity between crucial steps, they don’t just save time; they help ensure your results are correct.
Next time you move to the equilibration phase, take advantage of the auto-fill feature. It’s a quiet addition that makes your workflow noticeably more fluid.
➡️ Learn more about the NVT Equilibration process in the official documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.