GROMACS Wizard – Applying custom parameters

This section is a part of the GROMACS Wizard tutorial.

For each of the Energy Minimization, NVT Equilibration, NPT Equilibration, Production Molecular Dynamics Simulation steps you can provide custom molecular dynamics parameters using the graphical user interface or by loading them from an existing GROMACS molecular dynamics parameter file (an .mdp file).

By default, these parameters are populated with their default values. To inspect or modify them, click the All… button present in each of the aforementioned tabs (steps). Once 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 other GROMACS molecular dynamics parameters can be accessed by clicking on the button All….

The parameters are grouped as in the GROMACS documentation: Molecular dynamics parameters. You can inspect them by going through them. Each parameter has a tooltip which you can see by hovering above the parameter.

Not all of the molecular dynamics parameters are present in these advanced parameters windows, but they can be added or modified in the Additional parameters section. Please note that parameters provided in the Additional parameters section will overwrite those that are present in the advanced parameters window groups in case if the same parameters are specified.

You can modify parameters yourself or you can also load parameters from an existing GROMACS molecular dynamics parameter file (an .mdp file). To populate parameters from an .mdp file, click the Load from file… button and choose the .mdp file, please note that the .mdp options file needs to be for the same step. Even if almost all the parameters are present in the advanced parameters window, your .mdp file might contain some parameters which are not present here. In this case, they will be automatically added in the Additional parameters section where you can modify them if necessary. You can also copy-paste all the parameters present in your .mdp file in the Additional parameters section – they will overwrite those present in the advanced parameters window groups.

To apply your modifications of the parameters you have to click the button Ok button, while the Cancel button discards all the modifications that you have done in the advanced parameters window except the resetting to the default parameters.

You can also export parameters in an .mdp file by clicking Save as… button.

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

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

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

Comments are closed.