Choosing the right set of molecular dynamics (MD) parameters can make a significant difference in the fidelity and outcome of your simulations. But for many molecular modelers, manually editing and keeping track of .mdp files can be error-prone and time-consuming—especially when you’re frequently changing force field behaviors, time steps, or ensemble types across simulation stages.
The GROMACS Wizard within SAMSON offers a streamlined, graphical way to manage MD parameters, reducing the need to manually edit plain-text parameter files while still allowing advanced customization when needed. In this post, we’ll focus on how to use the advanced parameters window to apply custom settings for different simulation steps such as Energy Minimization, NVT, and NPT Equilibration, and Production Molecular Dynamics.
Why this matters
MD simulations often involve tweaking parameters like temperature coupling, cutoff schemes, or time integration settings tailored to specific systems. Navigating a large .mdp file by hand can be inefficient, particularly when parameters differ across simulation stages. The GROMACS Wizard solves this by letting you:
- Fill in standard parameters via dropdowns and input fields with tooltips.
- Access all adjustable options grouped logically just like in the official GROMACS documentation.
- Supplement or override parameters using an Additional Parameters section.
Best of both worlds: GUI and direct editing
Each simulation step tab (e.g., NPT Equilibration) includes an All… button that reveals advanced MD parameters in a separate window. Many users overlook this window, but it provides quick access to a full set of grouped options—for example, integrator options, thermostats, and constraints.
Not all possible MD parameters are listed in the GUI by default, but that’s okay—the Additional Parameters section lets you paste in any GROMACS-compatible setting. These values override those displayed elsewhere, ensuring experienced modelers maintain control without losing the convenience of a structured interface. This approach is particularly handy if you’re working from templates or publications that provide .mdp snippets.
Load, export, revert, repeat
If you have an existing .mdp file (a common situation when reusing protocol settings across different projects), you can load it directly by clicking Load from file…. The parameters are automatically parsed and populated, even those not initially present in the interface, which get added to the Additional Parameters section.
You can also export your setup via Save as… to generate a new .mdp file for use elsewhere. Don’t worry about experimenting—if things go wrong, use Reset to revert to default values or Cancel to discard changes made during the session.
Pro tip: Use the tooltips
If you’re unsure what a parameter means, hover over it. Each field is equipped with a tooltip offering short explanations pulled from the GROMACS documentation. For complete definitions, there’s always the full GROMACS parameter guide.
Once you’re done adjusting, press OK to apply your changes. SAMSON remembers your settings the next time you launch it, so you don’t lose progress even across sessions.
To learn more about using custom parameters in the GROMACS Wizard, visit the complete 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 download SAMSON at https://www.samson-connect.net