Before you hit the “Run” button on a molecular dynamics simulation, one seemingly small but critical decision can save you hours of confusion: selecting the correct input structure. If you’re using GROMACS Wizard in SAMSON for an NVT Equilibration run, supplying the appropriate .gro file is essential to ensure your simulation runs smoothly.
Here’s a practical guide to help you avoid one of the most common pitfalls in molecular modeling workflows—choosing the wrong input file, leading to errors, unstable simulations, or misleading results.
Why this step matters
Your input GRO file defines the molecular coordinates and box dimensions for the NVT equilibration. If you’re continuing from an earlier step like energy minimization, using the resulting file ensures continuity. But failing to select the correct file—perhaps using a non-minimized structure—can lead to an unstable start, errors in GROMACS, or unnecessary debugging.
Choose correctly (and quickly!)
GROMACS Wizard simplifies this with an auto-fill option. When you’re in the Equilibrate (NVT) tab and want to proceed from the last successful step, simply click:
Auto-fill.
This button grabs the output from the previous run—whether it’s from energy minimization or another NVT run—and auto-fills it as your input. No need to navigate folders or guess filenames.
What if you need custom input?
You can still select a different GRO file manually by clicking the … button and browsing to your file. This is useful when branching simulations, revisiting past runs, or organizing batch projects. Be sure the file you’re choosing has already been minimized or equilibrated correctly.
When mixing up files causes problems
Here are some symptoms you might encounter if the wrong input file is provided:
- Error messages from GROMACS about inconsistent box sizes or atom counts
- Simulations that crash immediately without producing output
- Unstable behavior like unrealistic temperature or pressure fluctuations
All these can usually be traced back to improper input—an error that is surprisingly common but easily avoided.
Best practice: consistent workflow
Whenever possible, move through your workflow sequentially within the same SAMSON session. This way, GROMACS Wizard retains context, and auto-fill options become your fast track. Especially in batch computations, maintaining consistent file naming and output tracking helps prevent confusion later on.
To sum up, be deliberate with your input selections. If you’re using the GROMACS Wizard in SAMSON, the auto-fill feature not only saves you time but adds reliability by automatically referencing the data from your last successful step.
To learn more about preparing input files for the NVT Equilibration step, visit the full documentation: GROMACS Wizard NVT Equilibration Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.