Molecular dynamics simulations are rarely one-size-fits-all. If you’ve ever needed to tweak temperature coupling, adjust time steps, or fine-tune constraints for your system, you’re not alone. Default settings are great for getting started, but real science often calls for customization. That’s where SAMSON’s GROMACS Wizard becomes especially helpful, letting you directly control and apply custom molecular dynamics parameters (MDPs) for each simulation step—without diving into command-line files.
Whether you’re running energy minimization, NVT or NPT equilibration, or production MD, SAMSON offers you a simple interface to tweak or completely redefine GROMACS parameters tailored to your system.
Where to Access Custom Parameters
In each step’s panel—energy minimization, equilibration, or production—you’ll see a button labeled All…. Clicking it opens an advanced parameters window specific to that stage:
From here, you can access grouped parameters organized similarly to the official GROMACS documentation. It’s a convenient way to identify and modify settings relevant to each simulation phase.
Understanding the Layout
Once the advanced window is open, you’ll find a structured layout, with each parameter accompanied by a tooltip when you hover your mouse over it. This helps clarify what each setting controls, even if it’s your first time encountering it.
Loading Your Own MDP Files
If you’ve worked on prior GROMACS simulations or received an .mdp file from a colleague, you can load it directly: click on Load from file… and select the file. SAMSON will do more than just show the entries—it will recognize which parameters are new and place them in a dedicated Additional Parameters section, where they automatically take priority over duplicated ones already shown in the interface.
This “load and override” approach makes it easy to reuse parameter sets across different projects or simply test alternate simulation setups without manually re-entering values.
Manual Edits and Exporting
You can freely modify or add new parameter lines in the Additional Parameters field. It’s a no-frills text area for directly inserting lines from a GROMACS .mdp file. You can also preview all current settings as plain text with View as text, and save them back to an .mdp file using the Save as… button.
Common Navigation Buttons
- OK: apply your new parameters.
- Cancel: discard your changes (though previously reset parameters will be kept).
- Reset: revert to default parameters.
Persistency and Reusability
One convenient aspect: SAMSON remembers your adjustments. Upon next launch, your custom parameters will still be there—saving time on repeated simulations or iterative tweaks.
When This is Especially Useful
This flexibility is especially useful when you’re experimenting with force field options, thermostats, or pressure coupling methods—or adjusting integration settings to stabilize difficult systems. Instead of juggling separate .mdp files externally, the SAMSON GUI gives you a unified and visual workflow.
To learn more, visit the original 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.