WHAM

Analysis > WHAM computes the potential of mean force (PMF) of an umbrella sampling run with pDynamo's Weighted Histogram Analysis Method. The umbrella sampling procedure itself is described in Umbrella Sampling; the quality of the windows can be checked with the Umbrella Sampling Browser.

The window (Figure 1)

• System and PMF type (1D or 2D).

• Bins [RC1] (and Bins [RC2] for 2D): the number of histogram bins along each reaction coordinate (default 100).

• Log frequency, Maximum iterations (default 1000) and RMS Gradient Tolerance (default 1.0e-3): control the iterative WHAM solution.

• Temperature: the temperature of the simulations (default 300 K).

• Bootstrap errors: standard error and 95% confidence interval of the PMF by bootstrap resampling of the umbrella data (pDynamo's WHAM bootstrapping), with the number of resamples. Each resample repeats the WHAM solution, so it multiplies the cost.

• Trajectories: Add trajectory block adds the data of an umbrella sampling run (the restraint values of its windows, folder data_collection); several blocks can be combined. Clear list empties the list.

• Log file / Working Folder: the output name and folder. The PMF is written to a file ending in _pmf.log (in the wham folder of the run, where the Umbrella Sampling Browser finds it).

• Browse Windows... opens the run in the Umbrella Sampling Browser.

Click Run. The PMF is plotted and its profile (1D) or surface (2D) can be explored like a PES. For the SN2 reaction Cl− + CH3Br (AM1, 31 windows, k = 600 kJ mol-1 Å-2, 10 ps per window), WHAM gives a free energy barrier of about 60 kJ/mol at RC ≈ +0.34 Å, from the reactant complex at RC ≈ −1.10 Å (Figure 2).