One common source of frustration in molecular dynamics workflows is accidentally using the wrong input file when transitioning between simulation stages. This becomes especially problematic during equilibration steps where mismatches can cause runs to crash or yield incorrect results. In the GROMACS Wizard available through SAMSON, selecting the correct input structure for the NPT equilibration step has been streamlined with helpful shortcuts and clear options. Here’s a closer look at managing this step safely and efficiently.
Why this step matters
Before jumping into pressure equilibration via the NPT ensemble, your system must have already gone through energy minimization and NVT equilibration. But the key requirement for this next phase is: you must provide a valid input file resulting from a previous step.
Options for Input Selection
GROMACS Wizard provides two primary types of accepted inputs:
- A .gro file from a completed step such as minimization or NVT equilibration.
- A batch project that includes earlier computation results such as minimization or NVT runs.
Choosing the wrong file (e.g., providing a structure that skipped key preparatory steps) can affect system stability and lead to wasted compute time. Fortunately, SAMSON’s GROMACS Wizard offers features that make this easier and safer.
Use the Auto-fill Feature
If you’re continuing directly from a previous equilibration or minimization step, you can simplify your input selection using the auto-fill button:
Clicking on the small 
icon will automatically populate the path to the most recent valid output file—saving you time and helping ensure file consistency across steps. This works whether you’re using standard .gro outputs or batch project results.
Manual File Selection Still Supported
If your source file comes from a different session or custom pathway, GROMACS Wizard doesn’t box you into automation. Simply click on the … button near the file input field to manually browse and select the desired file. This gives you full control over the process, while keeping the risk of missteps low thanks to clear labeling and file expectations.
Visual Feedback
This process is also supported through helpful visuals that clarify what stage you’re in and what the expected input is.
These cues reduce confusion and promote a smooth transition from one equilibration phase to another.
Pro Tip for Advanced Workflows
Working with batch simulations? Provided your project batch has been correctly minimized or NVT equilibrated, the same input logic applies. The GROMACS Wizard detects and supports batch results, making it reliable even in multi-system workflows.
Input selection is one of those stages that’s easy to overlook, but critical to get right. Thanks to GROMACS Wizard’s combination of automation and flexibility, it’s now faster and safer to move between key simulation checkpoints.
To learn more about selecting input files and other features of the NPT equilibration stage, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.