One of the recurring pain points for computational molecular scientists is managing the multiple input and output files between different simulation steps. This becomes especially cumbersome when performing sequential operations like energy minimization followed by NVT and NPT equilibrations, where each step depends on precisely structured outputs from the previous one.
In the GROMACS Wizard provided by SAMSON, there’s a small but impactful feature that helps overcome this: the auto-fill button for input structures.
Why this matters 🧪
While this might sound like a small convenience, for those working regularly with molecular dynamics simulations, it simplifies an otherwise error-prone and repetitive file-selection process. If you’ve ever had to hunt down the right .gro file among dozens or remember which specific batch project was used previously, you know how easy it is to accidentally select the wrong one, stall your workflow, or compromise reproducibility.
How auto-fill helps
In the NVT Equilibration tab, after you’ve successfully performed an Energy Minimization, SAMSON’s GROMACS Wizard lets you automatically populate the input field for the next step using the auto-fill feature.
Clicking on the small auto-fill icon 
does two things for you:
- It supplies the correct GRO or project file generated in the previous step.
- It ensures consistency by avoiding manual path entry errors.
This is particularly useful when working with batch projects or if you’re iteratively running several simulation steps. Whether you’re minimizing, equilibrating (NVT or NPT), or running the full molecular dynamics production, SAMSON’s GROMACS Wizard helps you keep continuity.
Choosing between GRO files and batch projects
If you’re not using the auto-fill option for some reason, you can still select the input manually:
- Use a GRO file from a previous minimization or equilibration.
- Select a batch project created during previous workflows.
The wizard supports both, recognizing the appropriate input sources regardless of your workflow.
Bonus: Maintain momentum
With the input loaded automatically, you can spend less time managing your simulation files and more time analyzing your results. It’s a simple part of a larger user experience design that aims to make molecular modeling and dynamics more accessible and less distracting. And if you find that your system hasn’t reached the target temperature after the first equilibration, simply run NVT again — the auto-fill button will still point you to the latest output.
To learn more about input selection and NVT equilibration using the GROMACS Wizard in SAMSON, refer to the full documentation here:
https://documentation.samson-connect.net/tutorials/gromacs-wizard/nvt-equilibration/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.