Before running a molecular dynamics simulation, equilibration is a critical step to prepare your system properly. But here’s the catch: many users—whether beginners or advanced—often spend unnecessary time managing input files and parameters for NVT equilibration. If you’re using the GROMACS Wizard Extension in SAMSON, there’s a streamlined shortcut that could make your workflow much more efficient.
This post focuses on one surprisingly useful, but easily overlooked feature: choosing input structures for NVT equilibration more efficiently.
Why input structure selection matters 🧩
Your molecular system has just gone through energy minimization. Now you want to run the NVT equilibration to stabilize its temperature—but which file do you use? Should it be the output .gro file, or a batch project? Where did you last save it? What if you’re running in batches?
These are more than minor nuisances, especially if you’re working with complex systems or running multiple jobs in sequence. Input file mismanagement is a common source of errors or delays.
A few clicks to the right input
In the GROMACS Wizard Extension, the NVT Equilibration tab has a user-friendly way to help choose your inputs.
- You can manually specify the input
.grofile or batch project. - But better yet, you can use the Auto-fill button that automatically selects the output from your last successful task—say, energy minimization. This feature is especially powerful when working with sequential workflows.
Want to browse manually? The … button lets you locate the desired .gro file easily.
What’s really convenient here is that GROMACS Wizard maintains continuity between steps. No need to leave the interface or dig through directories—the Wizard knows your last output and offers it to you ready-to-go.
Added bonus: Less guesswork, fewer mistakes
By auto-selecting the correct input structure, you reduce the risk of black-box mistakes—like selecting an incomplete file or the wrong structure. In larger simulation projects, that kind of error can cost you hours or even days. The Auto-fill feature also makes batching simulations more manageable, ensuring file consistency across steps.
This small functionality pays off especially well when scaling up work or collaborating across teams where consistent project structure is essential.
Need to go deeper?
You can read more in the full documentation, which also covers how to load parameters, edit index groups, and troubleshoot your equilibration steps:
Full NVT Equilibration Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.