When preparing a molecular system for simulation, it’s tempting to jump straight into running molecular dynamics. But, as every experienced modeler learns, skipping the pre-processing step can lead to frustrating errors or even incorrect results. If you’re using SAMSON with the GROMACS Wizard Extension, a dedicated pre-processing stage can simplify your workflow and help avoid preventable issues before entering the heavy computational steps.
The Pre-processing step in the GROMACS Wizard ensures that your molecular system is consistent and simulation-ready. Let’s look at why this step matters, what it does, and how it helps you start simulations on the right foot 🧪.
Why pre-process?
In most molecular simulations, there are several reasons things can go wrong:
- Missing atoms
- Incorrect connectivity
- Overlapping particles
- Improperly formatted input files
Pre-processing solves many of these problems for you—without diving into complex scripts or external tools.
What happens during pre-processing?
In the GROMACS Wizard Extension, the Pre-processing tool helps you perform the following actions:
- Validate molecular structure integrity: ensuring atoms and bonds are present and recognized.
- Assign atom types: including residue names and force field compatibility.
- Visual checks: lets you visually inspect the result so you can tweak or fix the structure before simulation.
- Set up topology generation for GROMACS: gets files ready for further preparation and minimization steps down the line.
This means you won’t have to go back and re-do simulations because of something preventable early on.
How does this help?
For SAMSON users new to GROMACS—or anyone preferring a graphical interface instead of command-line back-and-forth—the pre-processing step enhances productivity by saving time and reducing human error.
Rather than spending effort debugging .top or .gro files manually, everything is bundled into a guided visual experience that fits into the SAMSON platform. It also guarantees that when you reach more compute-heavy steps—such as energy minimization or equilibration—you’re working with valid, simulation-ready systems.
Pro tip: don’t skip it
If you’re teaching molecular modeling, setting up pipelines for others, or running projects where time matters, pre-processing keeps everyone on the same page. Use it as a chance to make sure your structure makes sense chemically and physically—before launching long simulations.
Learn more and explore the full range of features at the official SAMSON tutorial page for the GROMACS Wizard: https://documentation.samson-connect.net/tutorials/gromacs-wizard/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here: https://www.samson-connect.net