If you’ve ever run into issues at the start of an equilibration step in GROMACS, you know how frustrating it can be to realize that the problem was simply an incorrect input file path or format. This is particularly common during the NVT (constant Number of particles, Volume, and Temperature) equilibration phase. Starting with the right input structure isn’t just a prerequisite—it’s what determines whether your job runs smoothly or throws errors right away.
The GROMACS Wizard in SAMSON simplifies equilibration workflows, but it still relies on valid and properly formatted input files. Here’s a focused look at selecting the right input structure for NVT equilibration to help you save time and avoid avoidable troubleshooting.
What kind of input structure do you need?
During the NVT Equilibration step, the GROMACS Wizard requires either of the following:
- A GRO file from the previous minimization step or a previous equilibration run.
- A minimized batch project. These are especially useful if you’ve been running batch computations and want to maintain continuity across multiple systems.
Reduce risk with the Auto-fill button ⚙️
If you’re continuing directly from a recent minimization or equilibration step, the auto-fill button is your best friend. This small but crucial button (
) automatically fills the input path for you by using the results from the previous valid step.
This truly saves time and reduces human error. Instead of manually browsing for the latest GRO file—or worse, using an outdated one—you can get started in seconds.
Manual selection is available too
If you need to choose a specific GRO file—maybe for a different branch of your workflow—you can always do that by clicking the … button. This opens a file dialog to browse and select the exact file you need.
Handling errors: Better safe than sorry
Selecting the wrong structure can lead to errors ranging from simple file-not-found notifications to more complex mismatches in atom counts or topology. Before proceeding to run your simulation, take a moment to verify:
- The GRO file is the result of a successful previous step.
- Your topology corresponds to the structure provided.
- You’re not accidentally reusing an outdated or incomplete batch project.
Takeaway: Start strong by selecting right
This attention to input selection may sound like a detail, but it’s actually foundational. A correctly selected input structure minimizes runtime errors, avoids rework, and gets your simulations running faster.
To learn more about input selection and the full NVT equilibration process in GROMACS Wizard, visit the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.