Adapting molecular dynamics simulations to specific systems often requires precise control over simulation parameters. However, editing .mdp files manually or ensuring consistency across simulation steps—like energy minimization, NVT/NPT equilibrations, and production runs—can be time-consuming and error-prone. If you’re working with GROMACS through SAMSON, there’s a streamlined solution: the GROMACS Wizard’s support for loading custom molecular dynamics parameters directly from existing .mdp files.
This feature can be especially useful when replicating published simulations, comparing results across systems, or applying tuned settings from previous work. Here’s how it works, and how you can save time while keeping full control over your simulations 📂⚙️
Why use external MDP files?
In many molecular modeling workflows, you’ve already defined an optimized set of parameters in an .mdp file. Instead of reentering or cross-checking values one by one in the GUI of another tool, you can simply import your settings in SAMSON’s GROMACS Wizard and continue from there. Not only does this reduce error, it makes your workflow faster and more reproducible.
How to load MDP files in SAMSON
For each step of the simulation process—whether it’s energy minimization, NVT/NPT equilibration, or the production run—the GROMACS Wizard provides a straightforward way to apply custom parameters stored in an .mdp file:
- Open the relevant simulation step in the GROMACS Wizard.
- Click on the All… button to open the advanced parameters window.
- Click Load from file… and select your
.mdpfile.
The wizard will automatically match the file to the current simulation step and populate the relevant fields. If it contains parameters not directly exposed through the GUI, these will appear in the Additional Parameters section for you to verify or modify.
What happens behind the scenes?
When you load an external .mdp file, the GROMACS Wizard gives priority to those values over any existing ones within the interface. This ensures your exact settings are applied. Additionally, even parameters not explicitly included in the advanced GUI are accounted for in the simulation via the Additional Parameters field, giving you complete control without sacrificing usability.
Other options: manual edits and exports
You can also copy-paste MDP contents directly into the Additional Parameters section, or manually tweak individual fields after loading a file. Once you’re satisfied, use the Save as… button to export your adjusted parameters—a convenient way to document your simulation setup or share it with collaborators.
Why this matters
Customizing simulation parameters can deeply affect stability, convergence, and accuracy. SAMSON’s approach reduces friction for users who already have fine-tuned parameters or who prefer to experiment with advanced settings. Whether you’re prototyping a new system or reproducing previous results, this feature adds both flexibility and reliability to every stage of the workflow.
To learn more, including how default parameters behave, how tooltips can help explain parameters, and how to reset or discard changes, 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. You can get SAMSON at https://www.samson-connect.net.