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, and Production Molecular Dynamics Simulation steps you can provide custom molecular dynamics parameters (MDP) using the graphical user interface or by loading them from an existing GROMACS molecular dynamics parameter file (an .mdp file).

These parameters are populated with their default values. You can see some of the parameters directly in the tabs and the other parameters can be accessed by clicking on 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 parameters are grouped as in the GROMACS documentation: Molecular dynamics parameters. The set of available parameters is different for minimization, equilibration, and simulation steps.

Note: Each parameter has a tooltip which you can see by hovering above the parameter.

Not all of the molecular dynamics parameters might be present in these advanced parameters windows, but parameters can be added or modified in the Additional Parameters section. Note that the parameters provided there have priority over the same parameters present 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 that, 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 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.

You can also export parameters in 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 modifications of parameters that you have done except the resetting to the default parameters.

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

Note: the modified parameters are saved on closing SAMSON, so the next time you will have the previously saved parameters.

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.

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