You have prepared a molecular dynamics workflow in GROMACS Wizard, and the defaults look right—except for one or two settings. That small mismatch can create an awkward choice: change a parameter and risk overlooking something else, or abandon the interface and edit an MDP file by hand. The good news is that you can make targeted changes while keeping the rest of the setup visible and reviewable.
This is useful when you have a specific simulation reason to adjust a parameter, or when you need to reuse settings from a validated workflow. The key is to make changes in the right simulation step, understand which values take priority, and check what will be applied before running.
Start with the step you actually want to run
GROMACS Wizard provides parameter controls for energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics. Begin from the step you intend to run, rather than changing settings in a different step and assuming they will carry over. Each step has its own set of available parameters.
Keep the defaults unless you have a specific reason to change them. This helps limit the number of decisions you need to review and makes it easier to identify the effect of your own edits.
Use the full editor when a visible setting is not enough
The step tabs show commonly adjusted parameters. For a broader view, click All… to open the advanced parameter window. The controls are grouped in a structure that follows the GROMACS documentation, and hovering over a parameter displays its tooltip.
Not every GROMACS MDP option appears in this editor. If the parameter you need is missing, add it under Additional Parameters. Values entered there take priority over overlapping values elsewhere in the interface. That priority matters: if you set the same option in two places, the additional entry is the one to pay attention to.
Reuse an MDP file—and check what it brings in
If you already have an MDP file from another project or a validated workflow, use Load from file… to bring its parameters into the editor. Prefer a file intended for the same step, such as an equilibration file for an equilibration step. Parameters that do not have a matching control in the advanced editor are added to Additional Parameters, where you can review or edit them.
You can also paste MDP contents into Additional Parameters. Because those entries override overlapping values shown in the grouped controls, review the pasted text carefully before applying it. Loading a file is a convenient way to reuse settings, but it does not remove the need to check that they are appropriate for the step you are about to run.
Review before applying
Before you confirm your changes, use View as text to inspect the parameters together in a text window. You can save the current settings as an MDP file with Save as…, which can be useful for keeping a copy alongside your workflow.
- OK applies the modifications.
- Cancel discards parameter modifications, except for resets to default parameters.
- Reset restores parameters to their default values.
One detail worth remembering: modified parameters are saved when you close SAMSON, so previously saved settings will be available the next time you open it. If you want to find MDP files used for a simulation, look in the simulation results folder.
A practical review sequence is simple: select the intended step, make only the changes you need, check any entries under Additional Parameters, inspect the text view, and then apply the settings. After that, return to the GROMACS Wizard step and run the calculation with the reviewed parameters.
For the complete walkthrough, see the GROMACS Wizard guide to applying custom parameters.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.