Paper Citing NAMD - Abstract
Bonomi, M.; Barducci, A.; Parrinello, M.
Reconstructing the Equilibrium Boltzmann Distribution from Well-Tempered Metadynamics
JOURNAL OF COMPUTATIONAL CHEMISTRY, 30:1615-1621, AUG 2009
Metadynamics is a widely used and successful method for reconstructing the free-energy surface of complex systems as a function of a small number of suitably chosen collective variables. This is achieved by biasing the dynamics of the system. The bias acting on the collective variables distorts the probability distribution of the other variables. Here we present a simple reweighting algorithm for recovering the unbiased probability distribution of any variable from a well-tempered metadynamics simulation. We show the efficiency of the reweighting procedure by reconstructing the distribution of the four backbone dihedral angles of alanine dipeptide from two and even one dimensional metadynamics simulation. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 1615-1621, 2009
