Customizing molecular dynamics (MD) simulations often means editing .mdp files—those text files packed with GROMACS parameters that control temperature coupling, constraints, integrators, and more. If you’ve ever tried to integrate these hand-tuned files into a larger workflow, you probably know how tedious and error-prone it can get. SAMSON’s GROMACS Wizard offers a graphical interface to simplify this task, but what’s less known is how to apply your own parameter sets with just a few clicks.
Whether you’re replicating literature protocols or reusing configurations from past projects, SAMSON lets you inject your custom .mdp content directly into your MD setup—for Energy Minimization, NVT, NPT, and Production MD steps alike. Here’s how it works and what you need to know to streamline your workflow ⬇️
Where to find advanced MD options
When configuring a simulation step in the GROMACS Wizard, click on the All… button:
This opens a window presenting grouped parameters following GROMACS documentation structure. It’s an organized, readable alternative to scrolling through plain-text .mdp files.
Import your own .mdp file
If you already have an .mdp file from another project, you can load it using the Load from file… button. Parameters from the file will populate the GUI and, if some aren’t available in the main interface, they’ll be added to a special section called Additional Parameters. That means you’ll never lose a parameter—everything gets preserved.
Why this matters
Reconfiguring simulations from scratch each time is time-consuming, especially when validated simulation protocols already exist. Being able to do the following saves real time:
- Reuse consistent parameters across multiple steps or projects
- Quickly inspect or compare simulation setups
- Transfer simulation settings between collaborators via .mdp files
Tips to get the most out of it
- Hover for tooltips: Each parameter in the advanced panel has a tooltip—hover over it to get quick definitions.
- Use “View as text”: See the full list of parameters in one place before exporting or starting the simulation.
- All edits are saved: Even if you close SAMSON, your changes persist for later reuse.
- Load and edit: You can load an external .mdp, then tweak some settings directly in the GUI without touching the text file.
- Export your setup: Use Save as… to create sharable .mdp files from your current recipe.
What if a parameter isn’t listed?
Parameters missing from the default tabs can be added manually to the Additional Parameters section. This section has higher priority, so its values will take precedence over those set elsewhere in the interface. It’s ideal for experimenting with advanced flags or cutting-edge features not yet surfaced in GUIs.
A flexible, hybrid approach
SAMSON’s GROMACS Wizard lets you mix and match approaches: start with the defaults, import from existing files, and add final tweaks manually. It’s a simpler path that retains full control without being bound to scripting alone.
Learn more: Full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.