For molecular modelers working with GROMACS inside SAMSON, customizing molecular dynamics parameters can feel both powerful and a little daunting. Whether you’re fine-tuning your simulation or reusing parameter sets from prior projects, managing .mdp files effectively can save you hours and make your work far more reproducible.
The GROMACS Wizard in SAMSON offers a solution-oriented interface to apply custom parameters, not only through its intuitive GUI but also by loading and editing standard .mdp files. This blog post walks through the essentials, from quick edits to full parameter overrides, helping you take control of your simulations.
Why Custom Parameters Matter
Default molecular dynamics parameters are helpful, but real-world modeling often demands more. You might need to tweak energy minimization settings, apply particular constraints during equilibration, or replicate a published simulation exactly. These tasks require precise control over your .mdp configuration—something SAMSON facilitates in a user-friendly way.
Accessing and Editing Parameters in SAMSON
Inside the GROMACS Wizard, each step—be it Energy Minimization, NVT, NPT, or Production MD—has its own tab. Within these tabs, the most common parameters are visible by default. For full access, click the All… button.
This expands a window revealing grouped advanced parameters aligned with the official GROMACS documentation structure. Here’s a snapshot of what that looks like:
Power Users: Load, Modify and Prioritize
The interface supports three primary approaches to customizing your MD parameters:
- Edit directly within the GUI: Use tooltips for clarification and make changes inline.
- Load from an existing .mdp file: If you’ve already used GROMACS in other projects—or adopted settings from a published paper—you can load your file directly via the “Load from file…” button. Parameters not recognized by the pre-defined tabs are automatically added under “Additional Parameters.”
- Paste manually into Additional Parameters: Customize freely and ensure your settings override any conflicting values set elsewhere in the interface.
Extra Flexibility
Clicking on the View as text button lets you inspect all your parameters together. When you’re satisfied with your setup, you can export everything with the Save as… button—perfect for reuse or sharing.
Reset, Revert, or Apply Changes
You can always restore default settings using the Reset button. If you change your mind midway through editing, Cancel will revert changes except for previously restored defaults. To finalize your changes, click OK.
Need Persistent Settings?
Any changes you make are saved automatically when you close SAMSON. So next time you launch it, your custom parameters are right where you left them.
All this makes parameter management in SAMSON accessible without sacrificing depth. Whether you’re new to GROMACS or a seasoned practitioner tracking every nanosecond of your simulation, balancing interface-guided changes with deep customization allows you to focus more on the science and less on editing config files manually.
To learn more, visit the original documentation page: Applying custom parameters in the GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.