One of the recurring bottlenecks for researchers running molecular simulations with GROMACS is managing input files across multiple stages: preparation, energy minimization, equilibration, and production. Errors often arise when selecting outdated or mismatched input paths, especially in multi-step workflows or large batch simulations. If you’re using GROMACS Wizard in SAMSON, there’s a simple feature that can help you avoid this issue — the auto-fill path function.
This small but impactful option eliminates manual guessing by automatically inserting the appropriate input structure path from the previous pipeline step. Here’s how it works:
What exactly does “auto-fill” do?
After completing the Preparation step, GROMACS Wizard lets you move seamlessly into Energy Minimization. When prompted to select the input GRO file or batch project path, you don’t need to manually browse through your file system or remember folder names. Simply click the auto-fill button:
This button fetches the GRO file or batch project path from your last successful step.
Why it matters✔️
- Prevents file selection mistakes — No more mixing up batches or GRO files with outdated topologies.
- Speeds up your workflow — Transitioning from one step to the next takes seconds.
- Keeps things reproducible — Ensures consistency between preparation and minimization.
Using the auto-fill button in practice
Here’s what you’ll see in the Energy Minimization tab:
Besides the auto-fill button, there’s still a … button to manually choose the input file if needed. But on most occasions, especially during repeat testing or multi-step setups, the auto-fill option ensures a quicker and cleaner setup.
When it might not work
If no previous step was executed successfully in the current session, the auto-fill might not populate any path. In such cases, click … to navigate to your desired file manually. But once you know this shortcut exists, you’ll likely use it almost every session.
Bottom line
While seemingly minor, the auto-fill input path feature helps with one of the most error-prone parts of system preparation: file selection. If you’ve ever spent 20 minutes wondering why GROMACS can’t find your topology file, only to realize your path was pointing to the wrong directory, this feature is your new best friend.
You can learn more about running energy minimization in SAMSON’s GROMACS Wizard here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/energy-minimization/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.