Molecular dynamics simulations often require several steps before researchers can run a full production simulation. These include energy minimization, equilibration under various ensembles (NVT, NPT), and finally the production run itself. For those using GROMACS through the SAMSON GROMACS Wizard, one common bottleneck is managing input files between these stages—particularly ensuring that the right files from the previous step are selected for the next one.
Managing paths to output structures like .gro files or remembering which batch project came from which equilibration step can become tedious and error-prone. Fortunately, if you’re using SAMSON’s GROMACS Wizard, there’s a practical feature that solves this problem: the auto-fill button for selecting input structures. It’s a small but highly efficient interaction design that can help streamline your workflow, cut down mistakes, and save time.
A Small Button with a Big Impact
When you arrive at the Production MD Simulation step in the GROMACS Wizard, one of the first tasks is to select the input structure. This input should come from either the NPT equilibration results or from a previous production run, typically in the form of a .gro file or a batch project.
Instead of manually navigating your folders to locate that file, just click the Auto-fill button. It’s represented by a small icon:
This feature automatically retrieves the appropriate file path based on the most recent successful step. Whether it’s a batch project or a single file from an NPT run, this action ensures the continuity of your simulation pipeline without having to repeat file selection every time.
Why This Matters
For molecular modelers and simulation practitioners, workflows can quickly grow complex. Switching between project folders, second-guessing which file to use, or accidentally selecting an older file can all lead to wasted time—or worse, invalid results.
The auto-fill functionality simplifies this. It adheres to the natural left-to-right workflow of the Wizard tabs and encourages consistent project management. Plus, it reduces your mental load during simulation setup by eliminating repetitive tasks often prone to user errors.
You Still Have Control
If for any reason you want to use a different structure as your input, you can still click on the … button to open the file dialog manually. But for most cases following a linear tutorial or pipeline, the auto-fill gives the right file and lets you move forward confidently.
Especially when working on batch simulations or iterative refinements, having the tool anticipate your next step makes the overall experience more intuitive and less error-prone.
Learn More
This is just one of the many small usability features in the SAMSON GROMACS Wizard that make it easier to focus on scientific questions rather than software logistics. If you’d like to explore the full workflow for running a production MD simulation, you can read the official documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.