If you’ve ever found yourself scratching your head because your molecular dynamics simulation didn’t behave as expected during the NVT equilibration phase, you’re not alone. One of the most common causes? Incorrect or inconsistent input files.
Choosing the correct starting structure is essential for a successful NVT Equilibration. In the SAMSON GROMACS Wizard, a key part of this process is understanding what types of input you can use, how to choose them, and how to simplify this step without skipping crucial checks.
Understanding the valid inputs
The GROMACS Wizard allows two types of inputs for the NVT step:
- .GRO file — typically the output from the energy minimization step.
- A minimized batch project — another option if you’re managing multiple simulations.
Ultimately, the input must be a minimized structure. Applying NVT equilibration on a non-minimized system might cause numerical instabilities — like exploding atoms due to unfavorable geometries or unrealistic forces.
Use auto-fill to reduce mistakes ⚙️
If your system has just completed the energy minimization, you can use the auto-fill feature to save time and avoid mistakes. This small button automatically fills in the path to the most recent result:
Auto-fill button found next to the input file field
Once filled, you can double-check the source to ensure that it was indeed the result of a successful minimization. This works for both GRO files and batch project inputs.
Manual input still available
Prefer to set things manually? Click on the … button to browse and select any valid GRO file or project folder. This may be handy if you’re launching a new simulation based on earlier results, perhaps with different parameters.
Visual confirmation
After selecting your input, you can load the system using the Load button. This is more than a formality — it helps you confirm visually that you’re about to equilibrate the correct structure. This step is especially useful when working with systems that contain multiple molecules, solvent boxes, or membrane layers.
Why this matters
Simulation workflows often break at the transition between energy minimization and equilibration. Files get misplaced, folders get renamed, or settings aren’t carried over correctly. GROMACS Wizard reduces that friction, but only if users pay attention to this selection step.
Next time you run into unexpected results in your NVT phase — think temperature spikes, odd distributions, or job crashes — double-check that your input file points to a minimized system. Often, this one click can save an entire afternoon of rerunning calculations.
Learn more in the full guide to NVT Equilibration with GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON here.