Many molecular modelers working with GROMACS simulations face the same repetitive issue: each time you run a new molecular dynamics simulation—whether it’s energy minimization, NVT/NPT equilibration, or production MD—you often find yourself re-entering the same set of custom parameters manually.
Over time, this not only becomes tedious, but it also opens the door to mistakes and inconsistencies between runs. What if you could standardize and preserve your simulation settings across projects without tedious copying and pasting?
The GROMACS Wizard in SAMSON provides a practical solution to this pain through its flexible support for loading, editing, and saving molecular dynamics parameters (.mdp files).
Set Once, Reuse Many Times
Using the GROMACS Wizard, you can populate simulation tabs with default parameter values—or easily load them from a custom MDP file specific to your workflow. This can be done for each simulation step by clicking the Load from file… button and selecting an existing .mdp file.
If the file contains parameters not already shown in the tab’s interface, those values are automatically added in the Additional Parameters section and override default values. This feature aligns well with workflows that require consistent simulation conditions across different projects, or where institution-specific parameter sets must be applied.
View and Edit Everything in One Place
Clicking the All… button opens a complete view of all advanced parameters structured according to GROMACS documentation. From here, individual parameters can be toggled or updated, and helpful tooltips are provided for each setting just by hovering over them.
For example, during NVT equilibration, if you always use a specific thermostat and time step, you can input those values once and save the settings as a new .mdp file using the Save as… button. You’ll never have to manually replicate those changes again.
Simplify Sharing and Collaboration
Since you can export parameter sets and import them easily in subsequent projects, this also makes it simple to share simulation configurations with colleagues or collaborators. If someone sends you an .mdp file, just load it into the right step of your simulation setup—and the GROMACS Wizard will handle the incorporation.
Small Features That Help Accuracy
- Reset restores parameters to their default values.
- OK applies and saves changes.
- Cancel discards edits to avoid mistakes.
- View as text provides a complete snapshot of current parameters in plain text.
And here’s a helpful detail: even if you close SAMSON, your modified parameters are saved automatically, saving time the next time you open your project.
In addition, if you want to locate the exact values used for an earlier run, your simulation result folder retains the .mdp file used—making it easy to reproduce setups or document parameter choices.
To learn more about customizing GROMACS parameters in SAMSON, visit the official documentation page here: https://documentation.samson-connect.net/tutorials/gromacs-wizard/applying-custom-parameters/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.