If you’ve ever felt the friction of customizing molecular dynamics (MD) simulations in GROMACS, you’re not alone. Manually editing .mdp files, searching for the right flags, worrying about compatibility—all of this can slow down your work and distract you from your research goals. Fortunately, the GROMACS Wizard in SAMSON offers an efficient and user-friendly interface to apply and manage custom parameters without requiring you to write anything by hand. It’s particularly helpful in workflows where you need control but don’t want to start from scratch.
Why customize parameters?
The default MD parameters will run your simulation, but they might not be suitable for your specific system or purpose. For example, you may want to fine-tune temperature coupling methods, modify cutoffs, or change the integration time step. Having the flexibility to adjust these options visually can make your simulations both more precise and more accessible.
The Easy Entry Point
In SAMSON’s GROMACS Wizard, each step—Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD—comes with its own set of editable parameters. You can access many of them simply by clicking the All… button in the corresponding step tab:
This opens a window where the advanced parameters are neatly grouped according to the GROMACS documentation.
Three Ways to Update Parameters
- Manual Editing: You can click and edit values directly inside the interface. Tooltips are available if you hover over a parameter to get more information.
- Loading from an Existing File: If you already have a
.mdpfile, click Load from file… to import all or some of those parameters. Any extra parameters not found in the main window will be listed under the Additional Parameters section and will overwrite conflicting entries. - Typing Directly: You can copy-paste parameters into the Additional Parameters section, giving you flexibility to tweak even those options not explicitly shown in the advanced GUI.
Preserving Work
Worried about losing changes? You can:
- Click Save as… to export parameters to a new
.mdpfile. - Click OK to apply changes or Cancel to revert edits (excluding any resets to default).
- Click Reset to restore default values.
Even better: your customizations persist between sessions. When you reopen SAMSON, your last-used settings will be waiting for you.
Tip for Better Control
If you rely heavily on specific settings, consider creating a library of .mdp files tailored to each type of simulation. You can re-import them as needed and always fall back on a predefined state if something doesn’t work.
Where to find exported parameters
After running simulations, you can find the associated .mdp files in the result folders. These can serve as templates for future projects or for sharing parameter sets with collaborators.
To learn more, visit the original documentation page: Applying custom parameters in GROMACS Wizard.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.