Anyone working with molecular dynamics simulations using GROMACS has probably encountered this issue: you’re customizing your .mdp files, loading them into a graphical interface, and — suddenly — some of your expected parameters are nowhere to be found. Frustrating? Definitely. But let’s unpack why this happens and how the GROMACS Wizard in SAMSON can help solve it efficiently.
The usual pain point 🧪
When preparing simulations, molecular modelers often tweak GROMACS’s many molecular dynamics parameters. These .mdp files are ubiquitous — whether inherited from a previous project or downloaded from a benchmark study. However, graphical interfaces sometimes offer only a subset of these parameters, and missing values can lead to inconsistent simulations if you’re not careful.
In the SAMSON platform, the GROMACS Wizard tackles this by giving you both a structured view and a free-form way to inject your own parameters. But this flexibility comes with some hidden gems you might not be using to their fullest.
The key feature: Additional Parameters
Inside the GROMACS Wizard, when setting up any step — whether minimization, equilibration (NVT/NPT), or production — you have access to default or editable parameters grouped in tabs. But perhaps the most overlooked function is the Additional Parameters section. It’s your safety net.
Let’s walk through what happens when you load an .mdp file with uncommon or step-specific parameters:
- First, the interface loads supported parameters into structured fields.
- Then, it checks for any other parameters in the .mdp file not accounted for.
- These are automatically added to the Additional Parameters section.
This means nothing is lost — and you don’t need to search the documentation to re-enter missing fields.
How it looks
The GROMACS Wizard provides both accessible options and advanced flexibility. If you click the All… button (shown below), an advanced window appears with categorized parameters:
And here’s what editing those parameters looks like inside the advanced preferences window:
Some useful reminders 💡
- Every parameter in the interface includes a tooltip — just hover to learn what it does.
- If you paste parameters into the Additional Parameters section, they override the ones in the interface — avoid duplication.
- You can export your current configuration as a .mdp file to reuse it elsewhere.
Pro tip
If loading a partial .mdp file causes a mismatch (for instance, if you’re loading NVT parameters during production step setup), the Wizard still helps by sandboxing unknown parameters separately. Cleaner simulations with less stress.
Want to keep learning?
View the full documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.