One common source of frustration in molecular simulations is manually managing and entering the right files at each step in your workflow. If you’ve ever tried to launch an Energy Minimization step in GROMACS and struggled with locating the correct .gro file or batch project path, you’re not alone.
SAMSON’s GROMACS Wizard simplifies this with a handy feature: the auto-fill button. Here’s how you can avoid pathing mistakes and streamline your setup by taking full advantage of it.
Why correct file selection matters 🧬
When conducting energy minimization, the input system must not contain any steric clashes or broken geometries. Failing to provide the correct .gro structure often results in crashes or non-physical results. Worse, mistakes often go unnoticed until later, leading to wasted hours—or days—of simulation time.
To launch the Energy Minimization effectively in the GROMACS Wizard (after preparing your system), you’ll be asked to input either:
- A
.grofile from the Preparation step or a previous Energy Minimization. - A batch project path that was already prepared.
Manually navigating your folders to find the exact right file is possible—but error-prone. That’s where auto-fill comes in.
Auto-fill to the rescue
Instead of searching through folders, just click the auto-fill button, shown below:
This small but powerful feature detects the best matching input file automatically based on the last successful step. No more guessing the right file extension, or wondering whether a path corresponds to the latest iteration. Especially in batch mode or when working on multiple projects, this can save a lot of time and significantly reduce setup errors.
Prefer choosing manually?
If you prefer being hands-on, you can still choose your input file manually by clicking on the … button next to the file selector. This gives you full control of which file to use, in case you want to launch energy minimization again with a specific modified structure.
When to use auto-fill
Auto-fill works best when you’ve just completed the Preparation step and want to move directly to Energy Minimization using that output. Even better, it handles both single and batch projects, making it suitable for different levels of complexity.
Seeing SAMSON’s GROMACS Wizard do this automatically might seem like a small detail—but it’s precisely these details that remove repetitive tasks and decrease runtime errors, especially when working with multiple conformations or different system sizes.
Takeaway
Auto-fill is an efficient tool to help you avoid manual errors and keep your simulation process smooth. If you’re running repeated projects or switching between multiple systems, this button can save minutes—or hours—each day by helping you avoid small mistakes that could otherwise break your workflow.
To learn more about setting up Energy Minimization in SAMSON’s GROMACS Wizard, check the full documentation: 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.