GROMACS Wizard – PMF Analysis

This section is a part of theĀ GROMACS Wizard tutorial.

This tutorial demonstrates how to compute the Potential of Mean Force (PMF) using the Weighted Histogram Analysis Method (WHAM) in GROMACS Wizard.

Switch to the WHAM Analysis tab in GROMACS Wizard.

Choose the project path or click on auto-fill if the previous project you ran was the Umbrella Sampling simulation. The project folder might be a result of the batch computation, and it needs to contain numbered subfolders each containing simulation results done for the same system with the same reaction coordinates.

GROMACS Wizard will load the information from the project on reaction coordinates (names and bounds), time, and temperature.

Choose the reaction coordinate from the list, modify the other options (custom bounds, custom time, energy units) if needed, and click “Compute“. Two graphs will be produced showing the PMF and the histogram. For big trajectories, the computation might take several seconds or minutes.

The histogram graph demonstrates how well the reaction coordinate space is covered and where additional computations might be needed.

Once the computation is done for the given reaction coordinate and parameters, the computed profiles, histograms, and plots are automatically saved in the “wham_results” subfolder in the project folder. So, when you switch between reaction coordinates in the list, it will use the already computed data for the given parameters.

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