Simulation parameters can make or break the success of a molecular dynamics (MD) run. Whether you’re doing energy minimization or running production simulations, getting those .mdp settings just right is essential. But if you’ve ever spent time tweaking GROMACS parameter files manually or struggled to trace how your settings change over time, you know how time-consuming and error-prone this process can be.
The GROMACS Wizard in SAMSON provides a graphical interface that lets you apply and customize MD parameters without leaving your simulation environment. This blog post focuses on how to apply custom molecular dynamics parameters directly within SAMSON—an approach that can save molecular modelers substantial time and headaches.
Common Pain Point: Confusing Parameter Files
In GROMACS, every stage of a simulation—minimization, NVT/NPT equilibration, and production—has its own specific .mdp file. Many users manage these manually, editing text files each time there’s a change. Misplacing or misconfiguring even one parameter can lead to failed simulations or distorted results. Wouldn’t it be better to do all of this in a structured interface, with tooltips and logical categorization?
Working with Parameters in SAMSON
The GROMACS Wizard lets you customize your parameters step-by-step via tabs for:
- Energy Minimization
- NVT Equilibration
- NPT Equilibration
- Production Molecular Dynamics
Each step provides a set of default parameters, which can be expanded by clicking the All… button.
This opens a detailed parameters window, grouped in categories similar to those in the GROMACS documentation. Here you can see and modify parameters directly, or use the Additional Parameters field to override any defaults.
Import, Modify, Export
You can:
- Load from file… – Import parameters from an existing
.mdpfile - Save as… – Export your custom configuration
- View as text – See the full parameter list in plain text
- Reset – Restore to default values
- Apply or Cancel – Validate or discard changes
Small Details That Make a Difference
Each parameter has a tooltip for additional clarification—just hover with your mouse. Not all GROMACS parameters are presented by default, but any missing ones from an imported .mdp file are added under Additional Parameters.
If you dream of reusing parameter sets across projects without having to re-edit them manually each time, this feature is for you.
Automatically Saves Progress
As a bonus, SAMSON saves your modified parameters when it closes, so there’s no need to re-do your work the next time you open it.
Finally, all .mdp files used in your simulations are saved in the simulation results folder—helpful for reproducibility and documentation.
To learn more about how to apply and manage custom parameters in SAMSON, visit the full documentation 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.