Computation of equilibrium densities in metastable dynamical systems by domain decomposition
S. Kube, M. Weber – 2008
Whenever the stationary density of molecular dynamical systems decomposes into almost invariant partial densities, its computation from long‐time dynamics simulations is infeasible within the available computer time due to the well‐known “trapping problem.” In order to avoid this computational difficulty, we suggest a domain decomposition approach that is similar to umbrella sampling methods. In contrast to standard umbrella sampling techniques, our decomposition forms a partition of unity such that the corresponding stationary density can be computed as eigenvector of some mass matrix. This approach has many advantages over traditional approaches used to unbias and recombine the umbrella sampling calculations. The theoretical analysis is illustrated by a two‐dimensional example.