One of the most common sources of errors during molecular dynamics simulations happens right at the start: providing the wrong input file. Whether due to typos, incorrect paths, or confusion between file types, this early mistake can become a frustrating blockage—especially during the NVT equilibration phase. Fortunately, GROMACS Wizard in SAMSON offers a couple of clever features that help prevent these issues before you even hit the run button.
Minimize input errors with auto-fill
When preparing for NVT equilibration, users are required to supply a structural input: typically a .gro file from the previous simulation step, such as energy minimization. Missing or incorrect input files can lead to cryptic runtime errors or waste time debugging simple path mistakes.
Here’s a helpful trick: GROMACS Wizard has an Auto-fill button (
) to automatically populate the input path from your previous step. This smart link not only fills in the file path but also ensures it’s the appropriate structure to continue calculations, i.e., a minimized structure or a recent equilibration file.
Manual selection for flexibility
If you know exactly which file you want to use—or need to refer to a batch project—you can still manually select the input by clicking the “…” button. This flexibility is useful when working on multiple project branches or testing different minimized start points.
Just make sure the file was properly minimized or derived from an earlier run. Using an unprepared structure can cause unintended simulation behavior during equilibration and make downstream analysis less reliable.
Reusing existing results the right way
Running multiple rounds of equilibration is not uncommon. If your system hasn’t yet stabilized at the target temperature, you may want to re-run NVT equilibration using the last successful output as the new input. Again, the auto-fill button comes in handy here—it detects the latest result and sets it up instantly, error-free.
These simple actions may save you time and frustration. Instead of tracking down why your job failed to start, you can focus on adjusting simulation parameters or analyzing what matters: your system’s behavior over time.
To learn more, see the full documentation: GROMACS Wizard – NVT Equilibration.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.