One of the recurring pain points in molecular modeling workflows is tracing file paths and making sure the right input is chosen for each simulation step. If you’ve used GROMACS or other molecular dynamics tools, you’ve likely experienced the frustration of launching a job that fails due to an incorrect or missing input file.
Fortunately, the GROMACS Wizard in SAMSON simplifies this process thanks to flexible and user-friendly input selection options during the Energy Minimization step.
Making input selection simpler
Whether you’re continuing from a previous minimization or starting after system preparation, the GROMACS Wizard gives you two clear input path choices:
- A GRO file, typically the result of a previous Preparation or Energy Minimization step.
- A batch project directory if you’re running several systems in parallel.
Here’s a visual overview of how to choose your input type inside the Minimize tab:
Quick tip: Auto-fill your input
If you’re moving sequentially through the simulation workflow in the same session, you can often use the smart auto-fill feature.
Click the auto-fill button 
to automatically load the correct input structure from the previous step.
This simple feature spares you from manually navigating your files or risking the use of an outdated version of your system. It’s especially useful in large projects or when you’re running batch simulations:
Need to select manually?
If the auto-fill isn’t suitable—maybe you’re revisiting an older project or want to try different starting points—you can still manually select a GRO file using the … button. This gives you full flexibility for inputs from any point in your workflow.
Why it matters
Incorrect or mismatched inputs are one of the most common pitfalls in MD simulation workflows. They’re time-consuming to debug and can lead to misleading results if unnoticed. The GROMACS Wizard helps address this by:
- Providing an automatic way to reference previously generated results.
- Displaying clear visual cues so you can quickly verify the selected input.
- Maintaining consistency across batch jobs, minimizing human error.
Tip for batch runners
If you’re working with many systems at once and using batch mode, knowing that the same input selection features apply can help streamline your entire workflow. You can switch between projects reliably, without worrying about mixing up files or directories.
To learn more about input selection and the full Energy Minimization process using the GROMACS Wizard, visit the official 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.