You’re setting up a molecular dynamics calculation, and most of the GROMACS Wizard defaults look right—but one parameter needs to change. Maybe you’re continuing a validated workflow, or you have an existing .mdp file you want to reuse. The challenge is not simply editing a value: it’s knowing where to make the change, what takes priority, and how to check the settings before running.
Here’s a practical workflow for customizing GROMACS Wizard parameters while keeping the changes reviewable.
Start with the simulation step you intend to run
Open the relevant step—energy minimization, NVT equilibration, NPT equilibration, or production molecular dynamics—and begin with its existing settings. Keep defaults unless you have a specific reason to change them. Parameters differ between these steps, so an MDP file intended for the same step is preferable when loading an existing file.
The step’s main tabs expose commonly adjusted settings. For a broader view, click All… to open the advanced parameter editor.
Find the right place for a parameter
The advanced editor groups parameters in a way that follows the GROMACS documentation. Hover over a parameter to see its tooltip, which can help when you’re checking what a setting controls.
Not every GROMACS MDP option appears in the advanced editor. If the setting you need is missing, add it under Additional Parameters. This section also matters when values overlap: parameters entered there take priority over overlapping values displayed elsewhere in the interface. When copying settings into this section, review the final values so you know which setting will be used.
Reuse an MDP file without losing track of its contents
Choose Load from file… to bring in an existing .mdp file. Parameters recognized by the advanced editor can be reviewed there. Parameters in the file that aren’t represented in that editor are added to Additional Parameters, where you can inspect or modify them.
You can also copy and paste parameters from an MDP file into Additional Parameters. Those entries override corresponding values in the advanced parameter groups, so use this route deliberately rather than treating it as a neutral paste. For a quick audit, click View as text to inspect the parameters together. If you want to keep a copy of the configured parameters, use Save as… to export an MDP file.
Review before applying
Before confirming, check that you are editing the intended simulation step, that imported or manually added values are in the expected places, and that any overlapping values have the intended priority. Click OK to apply modifications. Cancel discards parameter modifications, except for resets to default parameters. To restore defaults, use Reset.
Modified parameters are saved when you close SAMSON, so they are available the next time you open it. Simulation results folders also contain the MDP files used for simulations, giving you a place to find the parameters associated with a run.
This small review habit can prevent a common source of confusion: thinking a value was changed, while another entry is actually taking precedence. For more details, see the GROMACS Wizard guide to applying custom parameters.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.