Potential of Mean-Force

Another useful structural property is the potential of mean-force (PMF). This property provides an energetic measurement of the binding strength between atomic species. This property allows for a direct analysis of the changes in binding strenght with respect to changing conditions. The potential of mean force is related to the radial distribution function (RDF) by

\[w_{\alpha \beta}^{(2)}(r) = k_\mathrm{B} T \: \mathrm{ln} g_{\alpha \beta}(r)\]

Implementation

In MDSuite, the potential of mean force is calculated directly from the RDF. In order to extract a scalar value from the PMF, we must find the minimum of the RDF and determine the PMF at that location. This is done applying a SavGol filter to smooth the RDF, before a peak finding algorithm is applied to determine the peaks in the RDF. These peaks are used as boundaries for a Golden-Section search which determines the minimum of the RDF. The radius of this minimum is then used to evaluate the PMF for the system.