If you’ve spent time setting up molecular dynamics simulations, you know how quickly your workflow can get tangled—especially when navigating multiple input files and output directories. One common friction point in this process is figuring out the correct input structure when moving from equilibration to production simulations.
In SAMSON’s GROMACS Wizard, starting your production MD simulation doesn’t have to involve a scavenger hunt through folders to locate the right .gro file. There’s a simple yet time-saving feature built into the interface: the auto-fill button for simulation inputs. 🎯
Why This Matters
During multi-step preparations—like energy minimization, NVT and NPT equilibrations, and eventually production MD—the GROMACS workflow relies on input files generated in previous steps. Mistakes here (like pointing to an incorrect or outdated file) can result in failed simulations or invalid results, wasting both time and compute resources.
SAMSON’s auto-fill function eliminates this user pain entirely. With one click, the software fetches the correct input file (either the final Structure file from equilibration or a previous production MD run), reducing errors and keeping your pipeline smooth.
How to Use It
On the Simulate tab of the GROMACS Wizard interface, you’ll see a section for selecting your input source. Right next to the input path field is an auto-fill button—a small icon that looks like this:
Clicking this button will populate the input field using the output from your previous step—whether that’s NPT equilibration or an earlier MD run. This also works seamlessly with both individual GRO files and batch projects.
Here’s how the full input setup area looks:
If needed, you can still manually choose a different input by clicking the … button and navigating to your file or batch project.
When to Use Auto-Fill
Auto-fill works particularly well when you are performing simulations in sequence. It ensures continuity in your project without introducing file mismatches. Anytime you’re moving from NPT to production MD—or running multiple productions—it makes the transition easier and more predictable.
Fast, Accurate, and Less Error-Prone
By reducing manual file selection, the auto-fill button not only makes you faster but also helps prevent mistakes—like selecting an incorrectly equilibrated structure or overwriting an old setup. And when you’re working on multiple projects, that peace of mind can be valuable.
Conclusion
This might seem like a small feature—but it speaks to a larger theme in SAMSON’s GROMACS Wizard: a streamlined user experience for molecular modelers who want to focus on the science, not the setup.
To explore more about the production MD simulation process and all related features, visit the full tutorial on SAMSON’s documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON at www.samson-connect.net.