GROMACS Wizard - Applying custom parameters

This section is part of the GROMACS Wizard tutorial.

Use this page when the default GROMACS Wizard settings are close to what you want, but you need to change one or more molecular dynamics parameters.

For each of the Energy Minimization, NVT Equilibration, NPT Equilibration, and Production Molecular Dynamics Simulation steps, you can provide custom molecular dynamics parameters (MDP) through the graphical interface or by loading an existing .mdp file.

Before you start

• Begin from the step you actually want to run.
• Keep the default settings unless you have a specific simulation reason to change them.
• If you already have an .mdp file from a validated workflow, you can reuse it here.

The tabs show the most commonly adjusted settings directly. For the full parameter editor, click All... ().

When clicked, a window with advanced parameters will appear. As an example, you can see a window with the advanced parameters for the NVT Equilibration step in the image below.

The parameters are grouped as in the GROMACS documentation: Molecular dynamics parameters. The set of available parameters is different for minimization, equilibration, and simulation steps.

Tip

Each parameter has a tooltip which you can see by hovering over the parameter.

Not all molecular dynamics parameters appear in the advanced parameter window. If a parameter is missing, add it in Additional Parameters. Values entered there take priority over overlapping values shown elsewhere in the interface.

You can modify parameters yourself or you can also load parameters from an existing MDP file, e.g., from some other project. For this, click the Load from file... button and choose the .mdp file. Please note that the MDP file preferably should be for the same step. If the provided MDP file contains some parameters that are not present among the parameters in the advanced parameters window, then they will be automatically added to the Additional Parameters section where you can modify them if necessary. You can also copy and paste all the parameters present in your MDP file into the Additional Parameters section - they will overwrite those present in the advanced parameters window groups.

You can also export parameters to an MDP file by clicking the Save as… button.

To view all the parameters in a text window, click the View as text button.

To apply the modifications, click the OK button.

To discard the modifications, click the Cancel button - this will discard all the parameter modifications you have made except for resets to the default parameters.

To restore the parameters to their default values, click on the Reset button.

Note

The modified parameters are saved when closing SAMSON, so the next time you open it, you will have the previously saved parameters.

You can always find .mdp files with molecular dynamics parameters used for simulation in the simulation results folder.

In addition to the comments provided, more explanations of the parameters can be found in the GROMACS documentation: Molecular dynamics parameters.