One of the most frequent pain points in molecular modeling is restarting a simulation step after modification or failure. If you’ve ever run a protocol, reached the equilibration stage, and then had to dig back through directories to track down a GRO file or the correct project to continue from, you’re not alone.
In GROMACS Wizard for SAMSON, Step 3—NVT Equilibration—smooths the process of selecting the right input. However, understanding exactly how it works can save you time and reduce errors, especially when you’re looping back after a run that didn’t quite stabilize.
Why Input Selection Matters 🧬
NVT equilibration is often the first phase of bringing your molecular system to the right simulation temperature. Getting this step right depends on providing a valid input structure—whether from the energy minimization step or a previous equilibration attempt.
According to the documentation, there are two primary input types you can use:
- A GRO file (typically produced after energy minimization or a prior equilibration step).
- A batch project (from a completed SAMSON batch computation).
What’s helpful is that GROMACS Wizard doesn’t just assume users know where their last GRO file is. It comes with an auto-fill button that intelligently proposes the last used structure:
Auto-Fill Button
After clicking it, the path is automatically populated based on the last output—whether from minimization or another NVT attempt:
This reduces one of the most error-prone steps in the process: input mismatches. No more browsing through folders guessing which GRO file to use.
Manual Selection Still Exists 👇
If for any reason you wish to override the automatic path (maybe you’re re-running an older job), that’s possible. Click the … button to manually browse and select your structure.
Pro Tip: Iterating NVT Runs Made Easier
If your NVT run doesn’t reach temperature stability, you can simply re-run the NVT step starting from the previous NVT results. The auto-fill button takes care of grabbing the correct structure—the one just created from that previous attempt.
Whether you’re equilibrating a protein, a solvated system, or both, this feature streamlines iteration, reduces setup time, and makes restarting simulations less frustrating.
Why It’s Worth Sharing 🧠
This small but smart usability feature alleviates a real pain point in day-to-day molecular modeling work. Sharing this tip with colleagues could save them from repeating a time-consuming or error-prone selection process, especially when handling multiple simulation runs back-to-back. Step 3 in the GROMACS Wizard is not just about running the NVT ensemble—it’s about running it painlessly.
Want to explore all the details? Learn more from the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.