Molecular modelers working with GROMACS know the importance—and the complexity—of setting the right molecular dynamics parameters. Whether it’s energy minimization, NVT/NPT equilibration, or production simulations, configuring .mdp (molecular dynamics parameter) files can become a time-consuming part of the workflow, especially if you need to repeatedly assign similar settings across multiple projects.
Fortunately, the GROMACS Wizard in SAMSON offers a practical solution: the ability to import existing .mdp files directly into each simulation step, and even fine-tune them within an intuitive graphical interface. If you’ve ever wished you could reuse an optimized parameter set without having to reconfigure every dropdown and checkbox, this feature might make a real difference.
Save Time with a Single Click
Instead of re-entering parameters manually, you can simply click the Load from file… button present in each of the main steps (Energy Minimization, NVT/NPT Equilibration, and Production MD). After selecting an existing .mdp file from a previous project, SAMSON automatically populates the relevant fields and even adds any non-standard parameters to an Additional Parameters section.
This is particularly useful when adapting templates or published settings for new systems. For example, you might want to reuse the equilibration parameters from a membrane protein simulation in your next ion channel study. No need to retype them or worry about typos.
What You See—And What You Don’t
To explore or tweak advanced settings further, click the All… button in any step tab. This reveals a window that organizes parameters into categories aligned with the GROMACS official documentation. Here, familiar sections like integrator, thermostats, constraints, output controls, and more are all present.
If the loaded .mdp file contains parameters not visible in this grouping, don’t worry—they’ll automatically appear in the Additional Parameters text field below the advanced window. These parameters override duplicates, and can even be added manually or by copy-pasting from a text editor.
A Transparent and Reversible Process
If you ever need to inspect the full list of parameters, just click the View as text button. Want to save your configuration for sharing or reuse? Use Save as… to export the settings into a new .mdp file.
Changed your mind? No problem. Click Cancel to discard recent modifications (except for resets), or Reset to restore the default values. Importantly, SAMSON preserves your custom settings even after closing the software, making it easy to pick up where you left off.
Conclusion
This functionality helps reduce repetitive work and minimizes the risk of configuration mistakes. If you’re working on multiple systems, across different environments, or as part of a research group with shared parameter files, importing .mdp files in SAMSON’s GROMACS Wizard can streamline your workflow considerably.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.