Anyone running molecular dynamics simulations with GROMACS has likely come across the challenge of managing and reusing .mdp files. These parameter files are essential, but editing them manually can be error-prone. More often than not, researchers keep a cluttered folder of outdated or incompatible .mdp templates, unsure whether they’re suitable for minimization, equilibration, or production runs. This small problem can quickly slow down workflows, especially when tweaking simulation settings or trying to reproduce someone else’s results.
The GROMACS Wizard in SAMSON offers a graphical and structured way to handle .mdp parameters across all simulation stages: Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD. Let’s look at how you can load, edit, and reuse parameter sets more cleanly—whether you’re working from scratch or adapting settings from another project.
Load existing parameters—no manual edits needed
If you already have a working .mdp file, click the Load from file… button in the SAMSON GROMACS Wizard interface. The wizard identifies which parameters in the file correspond to the current simulation step and automatically integrates them in the user interface.
Additional or unlisted parameters in your .mdp file are not discarded—they are preserved in a dedicated Additional Parameters section. Here’s the benefit: even advanced or custom simulation options remain visible and editable without breaking the interface defaults.
Make adjustments without fear of losing track
Within each step, clicking the All… button reveals an interface like the one shown below:
Each parameter includes a tooltip for quick reference. Some parameters are organized according to their groups in the official GROMACS documentation, so users already familiar with the manual will feel at home. But even new users can experiment safely, thanks to the built-in reset, export, and preview tools.
Export everything you see—your next simulation is organized
Once you’ve finished configuring, you can export the entire parameter set in an MDP file by clicking Save as…. This is especially useful for saving step-specific parameter sets—like one file for heating, another for equilibrium, another for production—that you or your collaborators can reuse in future projects.
If all you want is a full-text version of your current settings, including both editor and additional parameters, clicking the View as text button will show everything in one place. You can then organize or archive parameter sets clearly without modifying the core GUI-defined values.
Why it’s helpful
This isn’t just a convenience—it’s a cleaner and safer protocol for parameter management, especially when simulations are part of a larger pipeline involving multiple collaborators or reproducibility requirements. Every change becomes traceable and intentional, reducing the risk of mismatched settings.
Ready to streamline your simulation setup? Learn more in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.