Constructing smooth potentials of mean force, radial distribution functions, and probability densities from sampled data.
In this paper a method of obtaining smooth analytical estimates of probability densities, radial distribution functions, and potentials of mean force from sampled data in a statistically controlled fashion is presented. The approach is general and can be applied to any density of a single random variable. The method outlined here avoids the use of histograms, which require the specification of a physical parameter (bin size) and tend to give noisy results. The technique is an extension of the Berg-Harris method [B. A. Berg and R. C. Harris, Comput. Phys. Commun. 179, 443 (2008)], which is typically inaccurate for radial distribution functions and potentials of mean force due to a nonuniform Jacobian factor. In addition, the standard method often requires a large number of Fourier modes to represent radial distribution functions, which tends to lead to oscillatory fits. It is shown that the issues of poor sampling due to a Jacobian factor can be resolved using a biased resampling scheme, while the requirement of a large number of Fourier modes is mitigated through an automated piecewise construction approach. The method is demonstrated by analyzing the radial distribution functions in an energy-discretized water model. In addition, the fitting procedure is illustrated on three more applications for which the original Berg-Harris method is not suitable, namely, a random variable with a discontinuous probability density, a density with long tails, and the distribution of the first arrival times of a diffusing particle to a sphere, which has both long tails and short-time structure. In all cases, the resampled, piecewise analytical fit outperforms the histogram and the original Berg-Harris method.
van Zon
Ramses
R
Department of Chemistry, Chemical Physics Theory Group, University of Toronto, 80 Saint George Street, Toronto, Ontario M5S 3H6, Canada. rzon@chem.utoronto.ca
Schofield
Jeremy
J