One of the common pain points in molecular dynamics workflows is managing input files — especially when moving through simulation steps like energy minimization to equilibration. If you’re using GROMACS Wizard within SAMSON, there’s good news: the platform provides multiple convenient and error-proof ways to select the correct input structure for the NVT Equilibration step without dealing with confusing file paths or risking mismatched files.
Typical errors during this phase stem from using outdated or incorrect .gro files, especially when simulations span several steps or are re-launched. These errors can delay your workflow and lead to confusing simulation results. Fortunately, GROMACS Wizard offers built-in features that help minimize these issues — and knowing about them can save you significant time.
Three ways to define your input structure
When launching the NVT Equilibration step, GROMACS Wizard expects either:
- A .gro file from the earlier Energy Minimization step or a previous equilibration run
- A batch project that already includes a minimized system
The user interface allows you to do this manually by clicking the … button and browsing to the correct file. While this may be useful in some cases, it adds potential for human error. If the file structure changes or you’re unsure of the last successful run, the wrong input could compromise the next step.
A smarter way: Use the auto-fill feature
To avoid these pitfalls, use the auto-fill button:
This button intelligently populates the input field based on your last successful project, whether it’s a .gro file or a batch project. It’s a small feature that solves a big problem: continuity between simulation steps without manual tracking.
This reduces friction in your workflow, especially if you’re re-running jobs, performing parameter sweeps, or automating tasks with batch computations. Auto-fill ensures you’re always working from the most recent valid state of your system.
Why it matters
Incorrect inputs can result in:
- Parameter mismatches
- Out-of-bound coordinate errors
- Inconsistent system definitions (e.g., solvent box mismatch)
These errors are often subtle and can lead to simulations that crash late into the equilibration or yield misleading results. For students and researchers alike, catching such issues early through automated input handling is a crucial advantage.
Additionally, the simplicity of the interface — just one click to load the correct file — boosts reproducibility and lowers the barrier for new users to get accurate results.
Flexibility for advanced users
If you need to override this system, manual input remains an option. This is especially handy when branching simulations, testing edge cases, or comparing parameter sets across multiple structures.
But for most workflows, the auto-fill functionality offers a balance between reliability and ease-of-use.
To explore more details about setting up and running the NVT Equilibration step with GROMACS Wizard, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.