A general framework for non-Boltzmann Monte Carlo sampling.
Non-Boltzmann sampling (NBS) methods have been extensively employed in recent years, mainly due to their ability to enhance ergodicity in simulations of complex systems. In addition, they make possible reliable computation of equilibrium properties (ensemble averages, free-energy differences, and potentials of mean force) over continuous ranges of thermodynamic conditions. In this work, we put forward a general and systematic framework for NBS methods that allows a single set of equations and procedures to be applied to diverse systems. Moreover, we show how to exploit simulation data most effectively by obtaining continuous profiles of any mechanical properties, including structural quantities not directly related to the ensemble parameters. Finally, we demonstrate the usefulness of the developed formulation by applying it to spin systems, Lennard-Jones fluids, and a model protein molecule (both in isolation and in the proximity of a flat wall).
School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA.
Charlles R A
CR
Abreu
Fernando A
FA
Escobedo
D000465:Algorithms; D000595:Amino Acid Sequence; D001703:Biophysics / Q000379:methods; D002627:Chemistry, Physical / Q000379:methods*; D006358:Hot Temperature; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
D011506:Proteins