One of the most common roadblocks in running production Molecular Dynamics (MD) simulations is selecting the correct input structure. A few missteps here can lead to errors mid-simulation or, worse, misleading results. Fortunately, the GROMACS Wizard in SAMSON offers a streamlined approach to make this process more intuitive and less error-prone.
If you’ve just completed equilibration and are ready to move on to production MD, the input structure you use is critical. This might sound simple, but in practice, modelers often juggle multiple simulation outputs and folders. Let’s demystify the options and the helper features available in the GROMACS Wizard to make your simulations both faster and more reliable.
Supported Input Types
When setting up your production MD run, GROMACS Wizard allows you to choose between two types of input sources:
- A GRO file — Typically, the structure resulting from the NPT equilibration or a previous production MD run. The GRO file contains atomic coordinates and box dimensions and is essential for initializing the simulation.
- A batch project — If you’re working with automated or high-throughput workflows, loading the result of a prior batch job is supported. This is convenient if you’re reusing similar systems or conditions.
Save Time with Auto-Fill
If you’re continuing from the previous NPT equilibration step, there’s no need to manually dig through folders to find the correct file. The auto-fill button 
can automatically populate the path field with the last result file. This not only saves time but reduces the chance you’ll load the wrong structure.
Prefer to select manually? Just click the … button to browse for a GRO file or project folder. Having control over your input eliminates ambiguity, especially when working across teams or long-running projects.
Why This Matters
The integrity of a production MD simulation depends heavily on the starting structure. Using the wrong configuration — for example, an equilibrated file from a different system or incorrect timestep output — can skew your resulting data. GROMACS won’t always catch this kind of mismatch before computation begins, making it vital that you double-check consistency across steps.
Final Thoughts
To ensure things run smoothly:
- Stick to a structured workflow (e.g., Energy Minimization → NVT/NPT Equilibration → Production MD)
- Use the auto-fill feature when proceeding directly from earlier steps
- Verify time step continuity across files if manually loading an input
Small improvements in how you select input structures can reduce errors and save valuable time down the line. Explore this feature in the complete documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.