When setting up molecular simulations, one common challenge is managing simulation input data between steps. It can be surprisingly easy to misplace a file, use the wrong structure, or re-run calculations that were already done, simply because of input mismatches.
In the GROMACS Wizard inside SAMSON, this situation has been streamlined — particularly during NVT Equilibration. Below, we’ll walk through how to choose your input structure correctly and efficiently for this step, and avoid common mistakes many molecular modellers make in their workflow. This can save both time and computational resources.
Starting from the Right Place
The NVT Equilibration phase requires input structures from a previously completed step. Typically, this is an energy-minimized structure generated in the earlier Minimization step.
You have two options here:
- A GRO file that is the result of the Minimization step or a previous equilibration run
- A batch project file that was either minimized or generated in a prior step
This flexibility helps you integrate with previous work or even resume simulations from a partial run. But selecting the right object matters. Using the wrong input could lead to incorrect dynamics, wasted compute time, and unreliable conclusions.
Let the Wizard Help: Auto-fill is Your Friend ✨
If you’re continuing a typical workflow, the fastest way to load the correct structure is with the Auto-fill button:
Clicking this will populate the input path with the output from your previously completed step — no need to remember file names or project folders. This reduces the chance of errors and keeps your work organized.
Prefer Manual Control?
If you’re revisiting an older simulation or want full control, you can always click the … button and select your GRO file or batch project manually. This way, you can easily branch out from a past project or compare runs with different parameters.
Common Risks to Avoid
✔️ Accidentally using a structure that hasn’t been minimized: Always make sure your input comes from the Minimization step or a successful earlier equilibration run.
✔️ Using the same input repeatedly without updating: It’s easy to click through defaults quickly. Take a moment to make sure the loaded file reflects the step you think you’re continuing.
Good Practices for a Reproducible Workflow
- Use consistent file naming conventions across steps
- Leverage the auto-fill feature when continuing standard workflows
- Confirm your input settings visually — SAMSON makes them clear in the interface
- Document which input structures were used at each step if working outside SAMSON
Spending just a minute to verify your input can help you avoid silent errors that only show up in later stages, like in inconsistent temperature behavior during equilibration.
For a detailed walkthrough of the full NVT Equilibration process in GROMACS Wizard, refer to the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.