Setting up a molecular dynamics (MD) production run can be tedious when juggling multiple input files from earlier workflow steps. That’s especially true if you’re dealing with projects that go through energy minimization, NVT and NPT equilibration stages. Any mismatched file or small path error can lead to frustrating runtime issues. But SAMSON’s GROMACS Wizard offers a helpful feature that streamlines this often error-prone step: the Auto-Fill input path tool. 🧬💡
In production MD simulations, you need to provide either:
- A GRO file from the previous equilibration step (e.g., NPT equilibration)
- A batch project folder resulting from a past MD run
Manually navigating your files to locate the right GRO or project file each time is not only time-consuming but risks introducing inconsistencies—especially when managing multiple simulations. Fortunately, GROMACS Wizard includes a simple and effective solution for this.
Why Use Auto-Fill?
If your production MD step immediately follows a successful equilibration (like NPT), there is an Auto-Fill button () that automatically populates the input file path. This saves time and prevents common startup mistakes like:
- Using the wrong or outdated GRO file
- Incorrect directory paths
- Human error in selecting the right batch project
When you hit the Auto-Fill button, GROMACS Wizard checks your workflow history and intelligently proposes the appropriate input—whether it’s a GRO file or a batch project—from the previous step. No digging into folders, no second-guessing which file is the latest.
Manual Option for Power Users
If you’d rather specify the input directly—for example, if you’re resuming a simulation from older data—you can also click the … button next to the input field and navigate to the desired source:
- Select a different GRO file
- Choose an existing batch project folder
Best Practice Tip
Whether you choose Auto-Fill or the manual route, always double-check that the linked input file is consistent with your desired simulation state. Using the Auto-Fill feature substantially reduces the chance of mismatched thermodynamic parameters (like pressure or temperature coupling) that typically cause simulation instability or require reruns.
Final Thoughts
Tiny missteps in simulation setup can lead to hours of debugging or failed jobs. The Auto-Fill function in SAMSON’s GROMACS Wizard simplifies the process by reducing those small but critical mistakes. It’s especially useful when you’re running multiple iterations or batch jobs where keeping all paths correct becomes increasingly difficult.
By integrating workflows more seamlessly, SAMSON helps researchers focus more on their systems—and less on file paths.
To learn more about setting up production molecular dynamics simulations in SAMSON’s GROMACS Wizard, visit the full documentation page: https://documentation.samson-connect.net/tutorials/gromacs-wizard/production-md/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download it from https://www.samson-connect.net.