Running molecular dynamics simulations often involves fine-tuning a complex set of parameters. Whether you’re optimizing for performance or adapting to a specific research protocol, manually editing a GROMACS .mdp file can be tedious and error-prone—especially when trying to track which parameters apply to which phase of the simulation.
That’s where SAMSON’s GROMACS Wizard provides a real benefit. It offers a streamlined way to apply custom molecular dynamics parameters at each simulation step—be it energy minimization, NVT equilibration, NPT equilibration, or production runs—right from a graphical interface. For many researchers, this can simplify workflows and offer a clear visual understanding of the parameters being used at each step. In this post, we’ll explore how to navigate and benefit from SAMSON’s advanced parameter customization system.
Why Customize in the First Place?
Default molecular dynamics parameters are often a good starting point, but there are many situations where custom settings are essential:
- You need to use parameters validated by a specific protocol or publication.
- You want to replicate conditions from previous research or experiments.
- You’re troubleshooting convergence issues during minimization or equilibration.
Working with Parameters in SAMSON
Each simulation step tab in the GROMACS Wizard displays key parameters. For other available parameters, click the All… button to open the advanced configuration window:
This window groups parameters according to the same sections found in the official GROMACS documentation. You can scroll through or search for specific options. Hovering over any parameter reveals a tooltip with helpful information.
Loading and Editing Parameters
A common need is to import an existing .mdp file. For instance, if you’ve run a simulation in another environment or are continuing a previous project, you can click Load from file… and import those settings directly. SAMSON will compare the imported file to its current interface and display any additional parameters in an Additional Parameters section.
That section allows you to:
- Manually type or paste new parameters.
- Modify any parameter (these will override the interface settings).
- Easily switch between detailed editing and GUI-based input.
Apply or Reset Your Changes
Once satisfied with your customizations, click the OK button to apply them. If you change your mind, use Cancel to discard your edits or Reset to restore the defaults.
Prefer working in plain text? The View as text button shows all selected settings as a single text document—ideal for record-keeping or manual tweaking.
Finally, if you’d like to save your setup for reuse, click Save as… to export everything into your own ready-to-load .mdp file.
Small Tweaks Without the Guesswork
Advanced users will appreciate the precise control. For beginners, having tooltips, grouped parameters, and a visual interface removes much of the guesswork. It’s a user-friendly bridge between manuals and code—and makes custom simulations faster and more consistent.
To learn more, check out the full documentation page: 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.