One of the recurring pain points for molecular modelers using GROMACS is managing and fine-tuning molecular dynamics parameters across simulations. Whether you’re running energy minimizations or full production MD simulations, adjusting .mdp files efficiently without making mistakes or interrupting your workflow is crucial.
The GROMACS Wizard in SAMSON simplifies this process by letting users apply custom parameters through an intuitive interface. Rather than digging into text files manually, you can modify parameters visually—either using built-in fields organized by simulation step, or by directly importing/exporting complete parameter sets.
Friendly for both beginners and advanced users
Every step in a typical MD workflow — Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD — comes with default parameter values in SAMSON. You can modify these in each corresponding tab. For parameters not shown by default, clicking the All… button (
) opens up the full set of advanced parameters.
Here, parameters are grouped following the organization found in the official GROMACS documentation. This ensures familiarity even if you switch often between text files and GUI.
Tooltips, editing options, and more
Confused about what a parameter means? Just hover to see a tooltip with a quick explanation—useful for anyone who’s not interested in memorizing all the details. For further customization, you can enter additional or overriding parameters in the Additional Parameters section.
For example, if your team uses a specific cut-off scheme or thermostat setting, just paste those lines into the editor. Any parameters added here will take precedence over the GUI values.
Import from or export to .mdp files
Already have a parameter set you’ve used in another project? Use the Load from file… button to import your existing .mdp file. If the file contains unknown parameters, they’re added under “Additional Parameters” so nothing is lost. This is particularly helpful when cloning projects or standardizing simulations across a team.
Once satisfied, you can export your settings as an MDP file with the Save as… button, enabling reuse or further tweaking outside of SAMSON if needed. Before applying changes, it’s good practice to check everything via the View as text mode.
Safe exploration, easy recovery
Uncertain about an adjustment? Hit Cancel to undo changes, or click Reset to return to default parameters. If you’ve settled on a configuration, pressing OK will apply everything. Modified settings are saved automatically when you close SAMSON and reappear the next time you launch.
Finally, all the simulation result folders contain the generated .mdp files, so you’re never left wondering what exact parameters were used.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.