One of the most common frustrations for molecular modelers working with GROMACS is managing simulation parameters — especially when you want to adjust them frequently across different stages like energy minimization, NVT/NPT equilibration, or production molecular dynamics. Editing raw .mdp files line by line is not only error-prone but also time-consuming. Wouldn’t it be nice to have a more intuitive approach?
Enter the GROMACS Wizard in SAMSON, which provides a graphical user interface that lets you apply custom GROMACS parameters at each simulation step without opening a text editor. Whether you’re experimenting with thermostats, adjusting time steps, or importing parameters from previous projects, the interface is designed to make your workflow easier and faster.
Step-by-step Parameter Control
Within each stage — Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD — you’ll find accessible tabs where key molecular dynamics parameters (MDP options) are already populated with default values. These can be a starting point, but what truly helps is the deeper configuration layer revealed by the All… button:
Advanced Parameter Editing Made Simple
Clicking the All… button opens a window where parameters are grouped following GROMACS documentation conventions. You don’t need to remember or look up what each field does — just hover over any parameter to see a tooltip with explanations.
Even when a specific MDP parameter isn’t in the default interface, you can add it manually in the Additional Parameters section. Here you can:
- Manually type or copy-paste MDP parameters
- Import a full parameter set from another
.mdpfile using the Load from file… button - Override existing parameters simply by re-defining them
This flexibility is particularly useful when running similar simulations with nuanced differences, or when reusing trusted parameter sets from the literature or old projects.
Save, Export, or Reset at Will
Once you’ve finalized your parameter set, several options are available:
- OK to apply changes
- Cancel to discard changes
- Reset to revert to default parameters
- Save as… to export parameters to a new
.mdpfile - View as text to see all parameters together in a single window
And good news: the parameters are saved with your SAMSON session, so you don’t need to reconfigure them every time you reopen the application.
A Small Convenience with Big Impact
Sometimes it’s small interface choices that add up to significant time savings—especially when your project involves dozens of iterative simulations. The ability to quickly load, adjust, and apply parameter sets visually means less context-switching and more modeling progress.
To learn more or try it yourself, you can follow the official documentation here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/applying-custom-parameters/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.