Anyone who uses GROMACS for molecular dynamics simulations knows that managing .mdp files can be time-consuming. These files control the behavior of your simulation, but editing them manually every time you switch between minimization, equilibration, and production phases is error-prone and often frustrating. What if you could streamline this process without ever leaving your modeling environment?
The GROMACS Wizard in SAMSON offers a powerful way to customize simulation parameters directly through a graphical interface—no more constant alt-tabbing between your text editor and terminal. Whether you’re setting up energy minimization, NVT or NPT equilibration, or the final production MD phase, SAMSON makes it easy to apply custom parameters without breaking your workflow.
What makes it easier?
Each simulation step in the GROMACS Wizard comes with a tab populated with default MD parameters. You’ll see the most common ones at a glance, and with one click on the All… button, you can view and edit the full list of advanced MD parameters.
Clicking opens an advanced parameters window, grouped following the familiar structure from the official GROMACS documentation—so if you already know your way around these options, the structure will feel intuitive.
More flexibility with Additional Parameters
If a specific parameter isn’t listed in the window, just add it to the Additional Parameters section. This space acts like an override and will take priority over parameters set elsewhere in the interface. Great for testing novel setups or importing parameters from other labs.
Other helpful features include:
- Tooltips on every parameter for quick reference.
- Load from file… lets you import any
.mdpfile, reducing the time spent replicating project settings. - Save as… to export your configuration and reuse it elsewhere.
- View as text mode if you prefer to double-check all settings line-by-line.
- Reset to restore original defaults, for cases when things get messy.
Persistent settings, less repetition
Worried about losing settings between sessions? Don’t be. Edited parameters are saved when you close SAMSON. When you return, your configurations are still there—ready for the next run.
This integrated approach saves time and helps reduce misconfigurations due to manual input errors. For researchers who routinely run multiple systems or large projects, it offers a smoother and more reliable way to manage complex parameter sets.
To learn more, visit the original documentation page: GROMACS Wizard – Applying custom parameters.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.