When you’re working on molecular simulations, every misstep in the pipeline can cost hours of time—and the energy minimization step is no exception. A common source of frustration among molecular modelers is selecting the wrong input file just before launching energy minimization. This can occur especially in batch operations or when switching between projects. Fortunately, SAMSON’s GROMACS Wizard offers tools to simplify this step and ensure you’re feeding in the right data.
Why Input Selection Matters
Energy minimization is designed to resolve steric clashes and correct geometry before moving into dynamics. If you feed in an incorrect or incompatible structure—for example, a file from a misaligned step—you risk failed computations or unreliable results. The input at this stage must be clean and consistent with the preceding steps in your simulation pipeline.
Two Ways to Provide Input
GROMACS Wizard gives you two main options to provide input for the energy minimization step:
- A .gro file, typically the output from the previous Preparation step or even a previous Energy Minimization run.
- A processed batch project, useful when running simulations on multiple systems.
To access this, switch to the “Minimize” tab in the GROMACS Wizard interface:
Using the Smart Auto-Fill Option
For those who want to minimize human error, the auto-fill feature greatly reduces the risk of selecting the wrong file. By clicking the auto-fill button 
, SAMSON will automatically detect and insert the correct input from the last run—be it a .gro file or a batch project.
This is especially helpful when you’re juggling multiple simulations or updating a workflow. It eliminates the need to manually track filenames or folder locations.
Manual File Selection
If needed, there is still the option to manually select your .gro file using the … button. This gives you flexibility if you wish to test different configurations or revisit older data. However, be extra cautious—double-check that the file corresponds to the preparation phase of your current system. Manual selection offers control, but also introduces room for mistakes.
Bottom Line
Getting the input right for energy minimization is critical for starting simulations on solid ground. Fortunately, SAMSON’s GROMACS Wizard not only offers flexibility but also builds safety nets into the workflow to prevent common errors. Whether you rely on auto-fill or stick to manual selection, double-checking your inputs will save you time and ensure your simulations remain scientifically sound.
Want to explore the full pipeline available in the GROMACS Wizard? Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.