Molecular dynamics simulations often require parameter adjustments tailored to the system at hand. For GROMACS users, editing these parameters typically means diving into the .mdp files manually—a task that, while flexible, can be error-prone and slows down experimentation. If you’re customizing simulations in SAMSON using the GROMACS Wizard, there’s a more user-friendly way to manage these parameters—without constantly switching to a text editor.
The GROMACS Wizard in SAMSON allows you to fine-tune molecular dynamics parameters directly within a graphical interface. This means you can modify the parameters for Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD all within the same environment where you build and manage your simulation project.
Quick Access to Defaults & Tooltips 🎛️
Each simulation step comes populated with default GROMACS parameter values, and you can view and update visible parameters immediately in the interface. For a more exhaustive list, simply click the All… button:
Advanced Parameter Window 🧪
This button opens an advanced configuration window grouped according to the GROMACS documentation structure. For instance, here’s what the NVT Equilibration settings look like:
Clicking through presents even more parameters neatly grouped, all with tooltips so you don’t have to memorize syntax:
When Parameters Aren’t Listed
Not every single possible parameter can be shown in the grouped UI. That’s where the Additional Parameters section comes in. You can type in any extra parameters here that you’d normally write into an .mdp file. Handy if you’re applying project-specific tweaks or using custom algorithms not part of the default set.
Reusing Parameter Files
If you already have a configuration you’re happy with from past projects, you can import it using the Load from file… button. SAMSON automatically parses and integrates parameters. Any new ones go into the Additional Parameters section, so everything remains editable inside the interface.
Saving Your Settings
You can also export your current parameters to an .mdp file using Save as…, so nothing is lost—and you’re ready to reuse a custom configuration elsewhere.
Other Handy Options
- View as text: Browse or copy the parameters in a plain text format.
- Reset: Revert to default settings in one click.
- OK and Cancel: Apply or discard your changes as needed.
And to make it smoother for ongoing work, SAMSON saves your custom parameters when it’s closed. So the next time you start it, you’ll be right where you left off.
With this integrated workflow, you get a more accessible and transparent way to manage molecular dynamics parameters—so you can spend less time fixing line syntax and more time running simulations.
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. To get started, download SAMSON here: https://www.samson-connect.net