Enhanced Sampling Algorithms
arXiv:1012.5726
Abstract
In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped in states of these energy local minima. Enhanced conformational sampling techniques are thus in great demand. A simulation in generalized ensemble performs a random walk in potential energy space and can overcome this difficulty. From only one simulation run, one can obtain canonical-ensemble averages of physical quantities as functions of temperature by the single-histogram and/or multiple-histogram reweighting techniques. In this article we review uses of the generalized-ensemble algorithms in biomolecular systems. Three well-known methods, namely, multicanonical algorithm, simulated tempering, and replica-exchange method, are described first. Both Monte Carlo and molecular dynamics versions of the algorithms are given. We then present various extensions of these three generalized-ensemble algorithms. The effectiveness of the methods is tested with short peptide and protein systems.
42 pages, 7 figures, to be published in "Biomolecular simulations: methods and protocols" edited by Luca Monticelli and Emppu Salonen (Humana Press, 2011)
References in corpus (33)
- Escaping free-energy minima
- An efficient, multiple range random walk algorithm to calculate the density of states
- Statistically optimal analysis of samples from multiple equilibrium states
- Simulated Tempering: A New Monte Carlo Scheme
- Multicanonical Ensemble: A New Approach to Simulate First-order Phase Transitions
- Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
- Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse
- Critical point and coexistence curve properties of the Lennard-Jones fluid: A finite-size scaling study
- A New Approach to Spin Glass Simulations
- Extended Ensemble Monte Carlo
- Optimizing the ensemble for equilibration in broad-histogram Monte Carlo simulations
- Multicanonical Chain Growth Algorithm
- Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem
- Studies of an Off-Lattice Model for Protein Folding: Sequence Dependence and Improved Sampling at Finite Temperature
- Domain-Wall Free-Energy of Spin Glass Models:Numerical Method and Boundary Conditions
- Parallel Excluded Volume Tempering for Polymer Melts
- Multicanonical Simulations Step by Step
- Replica-Exchange Simulated Tempering Method for Simulations of Frustrated Systems
- Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble
- Monte Carlo Simulations in Multibaric-Multithermal Ensemble
- Monte Carlo Study of the Phase Structure of Compact Polymer Chains
- Multi-Overlap Simulations for Transitions between Reference Configurations
- Residual Entropy of Ordinary Ice from Multicanonical Simulations
- Numerical Simulations of Spin Glass Systems
- Spin glass overlap barriers in three and four dimensions
- Effective Sampling in the Configurational Space by the Multicanonical-Multioverlap Algorithm
- Molecular dynamics of C-peptide of ribonuclease A studied by replica-exchange Monte Carlo method and diffusion theory
- Molecular dynamics, Langevin, and hybrid Monte Carlo simulations in multicanonical ensemble
- Free-Energy Calculations in Protein Folding by Generalized-Ensemble Algorithms
- Replica-Exchange Molecular Dynamics Simulations for Various Constant Temperature Algorithms
- Thermodynamics of helix-coil transitions studied by multicanonical algorithms
- Generalized-Ensemble Algorithms for the Isobaric-Isothermal Ensemble
- Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem