If you’ve ever run molecular dynamics simulations using GROMACS, you’ve likely encountered the long list of options in MDP (Molecular Dynamics Parameters) files. From integrators to thermostats, every choice influences your results, and getting all of them just right isn’t easy. Wouldn’t it be helpful to adjust these parameters visually, with helpful tooltips and real-time previews? That’s exactly what the GROMACS Wizard in SAMSON enables you to do.
This blog post highlights how you can use SAMSON’s GROMACS Wizard to apply and manage custom parameters at different simulation stages — without needing to edit raw text files, unless you want to.
Why Custom Parameters Matter
For molecular modelers, simulation accuracy often depends on fine-tuning specific parameters. When preparing a system for dynamics, for example, you might use distinct constraints and temperature coupling methods depending on the force field, solvent model, or research goal. Even steps like energy minimization, NVT, and NPT equilibration can require different setups.
Traditionally, customizing these parameters meant editing MDP files manually — which can be both error-prone and time-consuming, especially when starting from templates or merging input from multiple projects.
Visual Parameter Editing
In the GROMACS Wizard, each simulation step — including Energy Minimization, NVT Equilibration, NPT Equilibration, and Production MD — includes editable default parameters. To access the full list of available settings, simply click the All… button:
This opens a structured advanced parameters window, where values are grouped according to the categories defined in the official GROMACS documentation:
Each setting comes with a tooltip, which provides a quick reminder of its purpose — great for when you’re switching between projects and need a refresher.
Loading and Exporting MDP Files
If you already have a working MDP file from a previous project, you can load it directly into the wizard using the Load from file… button. The system intelligently matches with existing fields and places unmatched parameters into the Additional Parameters section — where you can still edit them manually.
Need to reuse the parameters later? You can export your current configuration to a new MDP file using the Save as… button.
Fallbacks and Recovery
Made changes you regret? The wizard includes Reset, Cancel, and OK buttons so you can safely test alternative setups without losing your original values. Even better: modifications are saved automatically when SAMSON closes — there’s no need to reconfigure everything next time you open your project.
No Parameter Left Behind
While the most commonly used parameters are displayed in the main interface, anything not visible can be added manually via the Additional Parameters section. Whether you’re testing a custom barostat or experimenting with free energy perturbations, you always have the flexibility to adjust your setup as needed, all in one place.
To learn more and explore the full documentation on how to apply custom parameters with the GROMACS Wizard in SAMSON, visit the link below:
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.