One of the subtle yet persistent challenges molecular modelers face during molecular dynamics simulations is input file mismanagement—especially during equilibration steps. When performing NVT Equilibration (constant Number of particles, Volume, Temperature), even a small mistake in choosing the right input structure can derail your entire simulation workflow.
The GROMACS Wizard in SAMSON offers a structured and intuitive approach to help avoid this. This blog post focuses on how to correctly provide the input structure when starting the NVT Equilibration step—a step that brings your simulated system to the desired temperature and stabilizes it. If you’ve ever wondered whether to select a GRO file or a batch project, or worried about mismatched files, this guide is for you. 🧪
Understand What Input the Wizard Needs
When beginning NVT Equilibration, the GROMACS Wizard expects one of two things:
- A GRO file from a completed energy minimization.
- A batch project file that has been minimized or includes prior steps.
If you’ve gone through the previous step, i.e., energy minimization, the easiest solution is to use the auto-fill button:
This button saves you from navigating through directories and figuring out filenames. One click and the Wizard populates the input path based on the most recent successful run.
Manual Selection and Best Practices
If you prefer manual control, use the … button to browse and select your GRO file. Just be sure it is:
- Output from a Minimization step or
- Result from a previous NVT or NPT Equilibration
Mistakenly picking an outdated or incompatible GRO file may result in errors down the line, from force-field mismatches to simulation crashes.
Pro Tip: Keep It Organized
Folder chaos is real. The GROMACS Wizard names result folders based on the step name and the launch time, like this:
2023_12_01_15_45_32_nvt
Use these names as time stamps and context hints to distinguish results files quickly. The auto-fill button uses this logic to track the most recent valid file.
What If You Still Encounter Errors?
If you’re seeing warnings during input loading, double-check that:
- The structure matches the expected topology and force field.
- No intermediate modifications to the GRO file were made that broke consistency.
The Load button (near the input file field) validates and previews the input—use it as a sanity check before launching your computation.
Conclusion
Small details in file selection can save hours of troubleshooting. By using the auto-fill features and understanding what types of inputs are expected, you’ll improve your NVT Equilibration runs and set up your system for accurate, smooth simulation steps downstream.
To learn more about the NVT Equilibration step and how input files are managed, visit the full SAMSON documentation at: NVT Equilibration Tutorial.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.