A molecular dynamics setup can be close to what you need and still require one important change: perhaps you are continuing a validated workflow, or a parameter is not exposed among the settings you usually adjust. The tricky part is making that change without losing track of which values will actually be used.
GROMACS Wizard lets you adjust parameters for energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics. You can edit commonly used settings in the tabs, open the full editor with All…, or load an existing .mdp file. A little care with the workflow can make custom settings easier to review and reuse.
Start with the step you mean to run
First, open the GROMACS Wizard step where you want to make a change. The available parameters differ between minimization, equilibration, and production simulation, so an editor for one step is not simply a universal list for every stage. Keep the defaults unless you have a specific simulation reason to change them; this helps keep the adjustment focused.
If you have an MDP file from a workflow you have already reviewed, you can load it with Load from file…. Prefer a file intended for the same kind of step. A file may contain parameters that are not displayed in the advanced editor; the Wizard adds those to Additional Parameters, where you can inspect or modify them.
Pay attention to parameter precedence
The most important detail when mixing interface settings and custom values is that entries in Additional Parameters take priority over overlapping values shown elsewhere in the interface. This also applies when you copy and paste MDP parameters into that section: they overwrite matching values in the grouped advanced settings.
That behavior is useful when a parameter is missing from the editor, but it also means a value visible in a regular group may not be the final value if the same setting is specified in Additional Parameters. When adapting an MDP file, review that section for duplicates and confirm which value you intend to keep. If a parameter is not listed among the available options, Additional Parameters is the place to add it.
Review before applying
Use the parameter tooltips for context while editing, and consult the GROMACS MDP options reference when you need more detail. The View as text button provides a text view of the parameters, which can help you review the set as a whole. You can use Save as… to export the parameters to an MDP file, for example to retain a copy alongside your project workflow.
Before clicking OK, take a moment to check that you are editing the intended simulation step and that any custom entries are deliberate. OK applies the modifications. Cancel discards parameter modifications you made, except for resets to default parameters. To restore parameters to their defaults, use Reset.
A practical sequence
- Open the Wizard step you plan to run.
- Keep the defaults unless you have a specific reason to change a setting.
- Open All… for advanced options, or load a suitable MDP file with Load from file….
- Inspect Additional Parameters, especially if you pasted or imported values, because they take precedence over overlapping settings.
- Review the parameters in text view, export an MDP file if useful, and click OK to apply the changes.
Modified parameters are saved when SAMSON closes, so they will be available the next time it opens. MDP files used for simulations can also be found in the simulation results folder, which may help when revisiting a previous setup.
For the complete instructions and related step-specific tutorials, see GROMACS Wizard – Applying custom parameters.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.