Paper Citing NAMD - Abstract
Sakuraba, Shun; Kitao, Akio
Multiple Markov Transition Matrix Method: Obtaining the Stationary Probability Distribution from Multiple Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1850-1858, SEP 2009
We herein propose the Multiple Markov transition matrix method (MMMM), an algorithm by which to estimate the stationary probability distribution from independent multiple molecular dynamics simulations with different Hamiltonians. Applications to the potential of mean force calculation in combination with the umbrella sampling method are presented. First, the performance of the MMMM is examined in the case of butane. Compared with the weighted histogram analysis method (WHAM), the MMMM has an advantage with respect to the reasonable evaluation of the stationary probability distribution even front nonequilibrium trajectories. This method is then applied to Met-enkephalin nonequilibrium simulation. (C) 2008 Wiley Periodicals, Inc. J Comput Chem 30: 1850-1858, 2009
