If you’re a molecular modeler using GROMACS through the SAMSON platform, you may have tried to customize molecular dynamics parameters for different simulation steps—only to discover later that some of your settings were not applied during the run. This can be confusing and frustrating, especially when working on fine-tuned simulations for energy minimization or equilibration.
Here’s why this happens and how SAMSON’s GROMACS Wizard actually handles custom parameters—plus ways to make sure your MDP settings are used exactly how you intended. This tip alone can save you hours of unwanted surprises. 🧪
Different levels of parameter control
In SAMSON’s GROMACS Wizard, each MD step (Minimization, NVT Equilibration, NPT Equilibration, and Production MD) comes with its own set of default parameters visible in the interface. You can:
- Edit key parameters directly in each tab.
- Click the All… button to access a more extensive set of advanced parameters.
How to be sure your custom parameters are used
Here’s the important part: there’s a designated section in each advanced parameters window called Additional Parameters. This section exists specifically to allow users to:
- Add parameters that are not present in the GUI.
- Override values set elsewhere in the interface.
This means that if you paste a block of MDP settings here—including parameters already visible in other parts—they will take precedence over those shown in the tabs above.
Tips for working with MDP files
If you prefer reusing an existing .mdp file, simply use the Load from file… button. SAMSON will import compatible parameters automatically, and any extra ones will appear under Additional Parameters. This is especially convenient when working with parameter libraries across different projects.
To validate or review your full parameter set before running the simulation, use the View as text option. For reproducibility, it’s a good idea to save your configuration with the Save as… button — especially after heavy customization.
Hover to learn
Not sure what a parameter does? Just hover your mouse over it. Each parameter includes a helpful tooltip that gives you a short description, saving you the trouble of endlessly searching through GROMACS documentation.
Note: Changes are stored when you close SAMSON. Your most recent configuration will be available next time you launch the wizard.
Final reminders
- Click OK to apply changes.
- Use Reset to revert to default values.
- Click Cancel if you’d like to discard your changes.
By understanding the behavior of the Additional Parameters section, you can avoid misconfigurations and ensure that your custom settings are used as expected during simulation stages. This flexibility is useful whether you’re tuning thermostats, altering time steps, or setting constraints.
Want to dive deeper or see more screenshots? The full documentation is available here: GROMACS Wizard – Applying Custom Parameters.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.