When working with molecular dynamics simulations using GROMACS, setting the correct input files for each step is crucial. Whether you’re handling a protein-ligand complex, a solvated biomolecule, or a batch of systems, ensuring pipeline continuity can be tedious. One commonly reported pain point—especially for beginners—is managing input files between steps. Small errors in selecting the correct .gro file may cause inconsistencies or failed runs.
In the context of the NVT Equilibration stage within the GROMACS Wizard in SAMSON, input selection has been made significantly easier thanks to the auto-fill functionality. This post will walk you through how to streamline your workflow by avoiding manual file pathing and making the most of SAMSON’s tools.
Why It Matters
After the energy minimization step, most modelers want to proceed directly to NVT equilibration. However, switching contexts or mis-clicking might easily lead to selecting the wrong output file or project folder. Worse, if you’re running multiple simulations or working from various directories, this increases the risk of feeding incompatible inputs downstream.
SAMSON simplifies this with a small but powerful feature: the auto-fill button.
How It Works
When you open the NVT Equilibration tab, you’re prompted to specify an input structure. Instead of hunting through directories, you can click the auto-fill button:
This automatically pulls in the correct path based on your most recent successful computation—whether it’s an energy minimization or previous equilibration run. It detects the session context and avoids the need for error-prone file navigation.
Here’s the section where this happens visually:
Alternative Manual Pathing (Just in Case)
For more control, users can also manually select a .gro file or batch project using the … button. This is helpful if you’re managing multiple systems in parallel or looking to re-use inputs from another project. But for most users following the typical pipeline, auto-fill is a clear time saver.
Consistent input management can improve reproducibility and reduce time spent debugging run failures. Particularly in batch runs or larger workflows where small mistakes can propagate, these small user-centric touches in SAMSON offer significant quality-of-life improvements.
Final Thoughts
If you ever wondered whether the input to your NVT equilibration step was correctly selected, you’re not alone. But with the auto-fill feature and a thoughtful UI design in SAMSON’s GROMACS Wizard, the chance for errors during input file selection can be dramatically reduced.
Learn more about NVT equilibration and workflow in SAMSON’s GROMACS Wizard documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.