Bayesian inference was used to obtain self-consistent estimates of free energies and position-dependent diffusion coefficients along complex reaction coordinates from molecular dynamics simulation trajectories. Effectively, exact solutions for the dynamics of a diffusive model were matched globally to the observed molecular dynamics data. The approach was first tested for a simple one-dimensional diffusion model, and then applied to the dihedral-angle dynamics of a peptide fragment dissolved in water. Both long equilibrium molecular dynamics simulations and short, appropriately initialized, replica simulations were used to sample the short-time dynamics of the peptide-water system. In both cases, accurate estimates of free energies and diffusion coefficients were obtained.

Position-Dependent Diffusion Coefficients and Free Energies from Bayesian Analysis of Equilibrium and Replica Molecular Dynamics Simulations. Hummer, G.: New Journal of Physics, 2005, 7, 034