A potential of mean force (PMF) can turn umbrella-sampling results into a profile that is easier to inspect—but only if the window data fit together and cover the reaction coordinate well. When a result looks surprising, the challenge is not just producing a curve: it is checking whether the input windows are the ones you intended and whether the coordinate has been sampled across the range.
GROMACS Wizard computes the PMF with the Weighted Histogram Analysis Method (WHAM). Its histogram plot is an important companion to the PMF profile: it shows how well the reaction-coordinate space is covered and can help identify regions where additional sampling may be needed.
Start with a consistent set of windows
Before opening the WHAM Analysis tab, finish an umbrella-sampling workflow. The input folder should contain numbered subprojects that belong to the same system and use the same reaction-coordinate definition. This consistency matters: combining mismatched projects can make it difficult to interpret the resulting profile.
If you have just run the umbrella-sampling step, you can use auto-fill to select its project path. Otherwise, choose the project path yourself, then check the folder organization before computing the PMF.
GROMACS Wizard loads the reaction-coordinate information, time range, and temperature from the project automatically. Treat that automatic loading as a helpful starting point, then confirm that the coordinate you want to analyze is selected.
Compute the profile—and inspect the coverage
In GROMACS Wizard, switch to the WHAM Analysis tab. Select the reaction coordinate from the list. If your analysis calls for it, adjust optional settings such as custom bounds, a custom time range, or energy units. Then click Compute.
The result includes two plots: the PMF profile and a histogram showing coverage of the coordinate space.
Read these plots together. The PMF is the profile you set out to obtain; the histogram helps you see where the underlying coordinate sampling is concentrated or sparse. If the histogram indicates weak coverage in a region, consider whether more sampling is needed there before relying on that part of the profile. The histogram is a coverage aid, not a substitute for evaluating whether the simulation setup and sampling are appropriate for your scientific question.
A practical check when the result raises questions
- Confirm the inputs: Are the numbered subfolders from the same system and reaction-coordinate setup?
- Confirm the coordinate: Is the selected reaction coordinate the one used for the windows you intend to combine?
- Review coverage: Does the histogram suggest that any part of the coordinate range may need additional sampling?
- Revisit the windows if needed: The recommended next step for insufficient coverage is to return to umbrella sampling and add or extend simulations for the relevant windows.
For large trajectories, computation can take several seconds or minutes. When it finishes, GROMACS Wizard saves the profiles, histograms, and plots in the project’s wham_results subfolder. If you later switch reaction coordinates, the tool reuses data already computed for the same parameters.
This workflow makes the histogram more than a secondary figure: it gives you a practical way to spot where the windowed data may not support the range you want to interpret. To follow the full procedure, see the PMF Analysis documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.