One of the most common friction points in performing reliable molecular dynamics (MD) simulations is setting up input files correctly for production runs. Whether you’re working with batch jobs or single simulations, one misstep when defining inputs—like pointing to an incorrect .gro file or using mismatched equilibration outputs—can cause days of delay or confusing errors.
The GROMACS Wizard in SAMSON offers a small but highly practical feature that can help eliminate many of these mistakes: the auto-fill button. 🧠
What Problem Does It Solve?
After running an NPT equilibration or a previous production run, you need to specify which structure to use for the next simulation. Finding the right file manually can be tedious, especially if project folders multiply quickly—or even worse, if files have generic names like confout.gro.
Misaligned or incorrectly referenced input files not only waste time but can also create scientifically invalid simulations if control parameters or initial conditions are mismatched.
The Auto-Fill Button: Small UI, Big Help
In the production MD step of the GROMACS Wizard, once you’re in the interface for selecting the input structure, you’ll see a button that looks like this:
Clicking it automatically fills in the path to the correct file or batch project from your previous successful equilibration or production run. This minimizes the risk of loading the wrong file and eliminates the need to dig through file paths or project folders.
When to Use It
- If you just completed a successful NPT equilibration in the same project
- If you’re launching a chained production MD simulation (i.e., a continuation of a previous one)
- If you’re using SAMSON’s batch project format and want to keep things consistent
Manual Override Still Available
If needed, you can always override the path or choose a specific file using the … button. But for everyday workflows and especially when quickly iterating simulations, auto-fill is a reliable first step and a great way to standardize your processes.
Good Practice: Confirm the Source
Even though using auto-fill minimizes manual errors, you should still take a moment to double-check that the input reflects the system and equilibration conditions you expect. For example, verify that the file was generated with the same thermostat and barostat settings carried over from earlier equilibration steps.
This feature is especially valuable when collaborating with colleagues or mentoring students: using auto-fill encourages a reproducible workflow and avoids confusion over file lineage.
Wrapping Up
The auto-fill button may seem like a small shortcut, but for many modelers juggling multiple systems or conducting batch simulations, it’s a significant safeguard against input errors. Next time you launch a production MD simulation in SAMSON’s GROMACS Wizard, give it a click—you’ll likely save time and ensure smoother runs.
To explore more features and deeper control over simulations, visit the full documentation for the Production MD step in the GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.