Selecting the right input files when moving from one molecular dynamics step to another can feel repetitive and error-prone. If you’ve spent time scrolling through directories, trying to remember the difference between several similar GRO files, you’re not alone.
That’s why the GROMACS Wizard within SAMSON includes a very useful—but often overlooked—feature: the auto-fill functionality for selecting input structures during NPT equilibration. This small option can streamline your workflow, reduce mistakes, and help you focus on simulation quality instead of file logistics.
Why Input Selection Matters
When launching NPT equilibration, you need to provide the correct data that defines your system’s current state. Typically, this will be one of:
- A GRO file from a previous step, such as energy minimization or NVT equilibration.
- A batch project that stores an entire sequence of steps and metadata.
Making a wrong selection here can mean rerunning steps, wasted time, or incorrect results. That’s where auto-fill comes in.
Using Auto-Fill for Seamless Transitions
The GROMACS Wizard automatically tracks your successful workflow history. When you’re at the NPT equilibration stage, simply click the auto-fill button next to the input field.
It looks like this: a small file icon with a downward arrow. When clicked, it populates the path to the most recent applicable GRO file or batch project used in the previous run.
This option helps ensure continuity, especially in longer workflows where each step feeds into the next. No more mismatching files or having to open a file browser just to find “the right one.”
Manual Overrides Still Available
Of course, you’re still free to select another file manually. Click the … button to browse and specify a different GRO file or batch project if needed. But for most users following the tutorial or executing step-by-step workflows, auto-fill is a reliable shortcut that helps you stay focused.
Practical Tips
- Always check that the auto-filled file matches your expectations, especially when testing new configurations.
- If you encounter unexpected results, verify the input project history from the Local jobs panel.
- Use consistent naming conventions in your project folders to simplify both automated and manual workflows.
Learning to use small automation features like this one can free up mental energy and reduce interruptions in your modeling process. It helps make GROMACS Wizard inside SAMSON feel less like a chore to operate—and a little more helpful every day.
For a detailed walkthrough of the NPT Equilibration step, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.