For molecular modelers using GROMACS, adjusting simulation parameters typically involves diving into .mdp files and memorizing configurations. This can become time-consuming and error-prone—particularly when repeating simulations with slight variations or collaborating across teams.
The GROMACS Wizard in SAMSON offers an intuitive way to apply and customize your simulation parameters, all from a structured user interface that reduces manual editing and helps avoid common errors.
Why parameter customization matters 🧪
Every simulation step in GROMACS—minimization, NVT equilibration, NPT equilibration, and production runs—requires different sets of parameters tailored to specific experimental conditions. These parameters determine how your molecular system behaves, from thermostat algorithms to cutoff distances.
Editing these manually every time slows down your workflow and makes sharing simulation configurations more difficult. The GROMACS Wizard in SAMSON changes that.
Visual parameter editing, made for scientists
Each simulation step in the wizard comes with pre-populated default parameters. You can tweak the most commonly used options directly in their respective tabs. To go further, just click the All… button:
This opens a panel of advanced parameters grouped similarly to the official GROMACS documentation. This structure makes it easy to navigate if you’re already familiar with .mdp files, but offers a friendlier route for those who aren’t.
Managing parameters: from load to export
You can take three approaches when customizing parameters:
- Modify directly: Click on any field and enter your desired value. Tooltips are available on hover for guidance.
- Load from an existing .mdp file: This is useful when reusing setups from past projects. Just click Load from file…. If the file contains options not found in the window, they’ll appear in the Additional Parameters section.
- Copy-paste entire content: Paste the full text of a .mdp file into the Additional Parameters box. This will overwrite existing settings where applicable.
You can also export your current settings to a new .mdp file by clicking Save as…. This allows easy sharing and helps maintain reproducibility in larger collaborative projects.
Smooth control over your simulations
Here’s what else you can do with this panel:
- Restore defaults using the Reset button
- Inspect all parameters without formatting using View as text
- Apply or discard changes via OK and Cancel
All changes are saved automatically when closing SAMSON—so your presets are available when you return.
The takeaway
If you’re accustomed to working directly with MDP files, the SAMSON GROMACS Wizard will feel refreshingly organized. And if you’re new to parameter tweaking, this interface will help you experiment without fear of wrecking your setup.
To learn more, explore the full tutorial page 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