A molecular dynamics setup can be almost ready to run—and still need one parameter changed. The tricky part is not always finding the setting; it’s knowing whether your edit will take effect, especially when values come from both the graphical controls and an existing .mdp file. A small, deliberate workflow can help you customize a GROMACS Wizard step without losing track of what you changed.
Start with the step you intend to run
Energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics use different sets of parameters. Open the parameter editor from the step you actually want to configure. If you have an .mdp file from a workflow that has already been validated, you can load it, but the file should preferably correspond to the same type of step.
Keep the defaults unless you have a specific simulation reason to change them. This is a useful way to reduce accidental changes: first identify the scientific or workflow need, then adjust only the relevant parameter or parameters.
Know where to look—and where overrides live
The step’s tabs show commonly adjusted settings. Click All… to open the advanced parameter window and browse a broader set of options, grouped in a way that follows the GROMACS parameter documentation. Hover over a parameter to see its tooltip.
Not every GROMACS MDP parameter appears in the advanced parameter window. If you need a parameter that is missing, put it in Additional Parameters. Pay attention to precedence: values in Additional Parameters take priority over overlapping values shown elsewhere in the interface. In practice, if the same setting appears in both places, check the Additional Parameters entry before assuming the visible grouped control is the value that will be used.
Import carefully; review the result
Choose Load from file… to bring in an existing .mdp file. Parameters in that file that are not represented in the advanced parameter groups are added to Additional Parameters, where you can review and edit them. You can also paste MDP parameters into that section; pasted values overwrite matching values in the advanced parameter groups.
That makes importing convenient, but it also makes a quick review worthwhile. After loading or pasting, look for duplicate settings and confirm that values in Additional Parameters are intentional. Use View as text to inspect the complete parameter set in a text window. If you want to keep a copy of the configured parameters, use Save as… to export them to an MDP file.
Apply, discard, or reset—three different actions
Click OK to apply your modifications. Click Cancel to discard the parameter modifications you made, with one important exception: resets to default parameters are not discarded. If you want to restore parameters to their defaults, use Reset. These buttons do different things, so choose based on whether you want to keep edits, undo edits, or return to defaults.
Modified parameters are saved when you close SAMSON, so they will be available the next time you open it. For later reference, MDP files used for simulations can also be found in the simulation results folder.
A simple pre-run check
- Confirm that you opened the editor for the intended simulation step.
- Check whether an imported file is for that same step.
- Review Additional Parameters for entries that may override grouped settings.
- Use View as text to inspect the full parameter list.
- Choose OK to apply, or Cancel to discard edits, remembering the reset exception.
This check does not replace choosing scientifically appropriate settings, but it can help prevent a parameter from being overlooked simply because it was entered in a different part of the interface.
For the full walkthrough, see the GROMACS Wizard guide to applying custom parameters.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.