Paper Citing NAMD - Abstract
Vitalis, Andreas; Pappu, Rohit V.
Methods for Monte Carlo Simulations of Biomacromolecules
ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY, VOL 5, 5:49-76, 2009
The state-of-the-art for Monte Carlo (MC) simulations of biomacromolecules is reviewed. Available methodologies for sampling conformational equilibria and associations of biomacromolecules in the canonical ensemble, given a continuum description of the solvent environment, are reviewed. Detailed sections are provided dealing with the choice of degrees of freedom, the efficiencies of MC algorithms and algorithmic peculiarities, as well as the optimization of simple movesets. The issue of introducing correlations into elementary MC moves and the applicability of such methods to simulations of biomacromolecules are discussed. A brief discussion of multicanonical methods and an overview of recent simulation work highlighting the potential of MC methods are also provided. It is argued that MC simulations, although underutilized in the biomacromolecular simulation community, hold promise for simulations of complex systems and phenomena that span multiple length scales, especially when used in conjunction with implicit solvation models or other coarse-graining strategies.
