Anyone working with molecular simulations knows the frustration of constantly navigating folders to locate the correct input files—especially when transitioning between simulation steps like energy minimization, NVT equilibration, and NPT equilibration. If you’re using the GROMACS Wizard in SAMSON, there’s a feature that can save you a surprising amount of time (and clicking): the auto-fill button for input structure selection.
Whether you’re running small molecule simulations or exploring protein dynamics, each GROMACS step requires as input either a .gro file or a batch project. Selecting the right one manually can be error-prone—and when you’re juggling multiple simulations or setups, it’s all too easy to pick the wrong file.
Why Input Selection Is a Common Friction Point
Input choices in molecular simulations are often:
- Spread across deeply nested directories
- Confusing when previous and current steps have similarly named files
- Prone to version errors if an outdated file is loaded
This is even more critical in workflows like NVT equilibration, where the input must reflect the most recent minimized structure or the outcome of the previous GROMACS step.
Simplifying with Auto-Fill
The GROMACS Wizard includes a smart feature that simplifies this process: an auto-fill button that detects the output of the last successful step—whether it’s a minimized structure or earlier equilibration—so you don’t have to search for it.
Here’s what it looks like:
Clicking this small but mighty button automatically fills in the correct structure path. It’s a small UI feature that can make a big difference when you’re managing multiple simulation projects.
More Options Still Available
Of course, you’re not restricted to auto-fill. You can choose an input file manually by clicking the … button to browse your system.
But when possible, the auto-fill option minimizes human error and helps reduce workflow interruptions—especially useful for iterative steps like repeated equilibration runs.
When to Use Auto-Fill
Use the auto-fill feature when:
- You’re proceeding immediately from a previous simulation step within SAMSON.
- You’ve already run a batch job or a prior local job and want to continue based on its output.
- You’d prefer not to search through simulation folders.
Save Time, Reduce Errors
This kind of thoughtful feature is especially appreciated in research environments where hundreds of simulations may need to be queued or repeated. By giving users a quick and accurate way to pass data from one step to the next, the auto-fill button contributes to cleaner workflows and fewer mistakes.
Want to see this in action or learn about the rest of the NVT equilibration setup? Check out the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get the platform at samson-connect.net.