Parallel Tempering Algorithm for Conformational Studies of Biological Molecules

Abstract

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides, Met-enkephalin. The numerical effectiveness of the new technique was found to be much better than traditional methods and is comparable to sophisticated methods like generalized ensemble techniques.

Latex, ps-files included; to appear in Chem. Phys. Lett

References in corpus (2)

• Generalized-ensemble Monte carlo method for systems with rough energy landscape
• Simulated Annealing with Tsallis Weights - A Numerical Comparison

Cited by in corpus (113)

• PLUMED: a portable plugin for free-energy calculations with molecular dynamics
• Parallel Tempering: Theory, Applications, and New Perspectives
• Multidimensional replica-exchange method for free-energy calculations
• Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration
• Enhanced sampling methods for molecular dynamics simulations
• A Biased Monte Carlo Scheme for Zeolite Structure Solution
• Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
• Enhanced Sampling in the Well-Tempered Ensemble
• Hamiltonian replica-exchange in GROMACS: a flexible implementation
• Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration
• Extended Ensemble Monte Carlo
• Optimized parallel tempering simulations of proteins
• Strict Detailed Balance is Unnecessary in Monte Carlo Simulation
• Resolution exchange simulation
• Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
• A Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes
• A self-learning algorithm for biased molecular dynamics
• Ensemble based convergence assessment of biomolecular trajectories
• Generalized Ensemble and Tempering Simulations: A Unified View
• The incomplete beta function law for parallel tempering sampling of classical canonical systems
• Parallel Excluded Volume Tempering for Polymer Melts
• Geometric integrators and the Hamiltonian Monte Carlo method
• Make life simple: unleash the full power of the parallel tempering algorithm
• Multicanonical Parallel Tempering
• Replica-Exchange Simulated Tempering Method for Simulations of Frustrated Systems
• Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
• Enhanced sampling and applications in protein folding in explicit solvent
• Phase diagram of the Ising square lattice with competing interactions
• Path integral virial estimator based on the scaling of fluctuation coordinates: Application to quantum clusters with fourth-order propagators
• Heat capacity estimators for random series path-integral methods by finite-difference schemes
• Location of the Potts-critical end point in the frustrated Ising model on the square lattice
• Optimal estimates of free energies from multi-state nonequilibrium work data
• Generalized Ensemble Simulations for Complex Systems
• From data to noise to data: mixing physics across temperatures with generative artificial intelligence
• Density of states of a binary Lennard-Jones Glass
• Analysis of the phase transition for the Ising model on the frustrated square lattice
• Monte Carlo Study of the Phase Structure of Compact Polymer Chains
• Efficient Stochastic Simulation of Chemical Kinetics Networks using a Weighted Ensemble of Trajectories
• Simulation via Direct Computation of Partition Functions
• Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications
• Strengths and Weaknesses of Parallel Tempering
• Phase changes in selected Lennard-Jones X_{13-n}Y_n clusters
• Efficient ab initio schemes for finding thermodynamically stable and metastable atomic structures: Benchmark of cascade genetic algorithms
• Structure of Si(114) determined by global optimization methods
• On Dynamics and Optimal Number of Replicas in Parallel Tempering Simulations
• Dual-Topology Hamiltonian-Replica-Exchange Overlap Histogramming Method to Calculate Relative Free Energy Difference in Rough Energy Landscape
• Reconstruction of silicon surfaces: a stochastic optimization problem
• Ratcheted molecular-dynamics simulations identify efficiently the transition state of protein folding
• Statistically optimal continuous free energy surfaces from biased simulations and multistate reweighting
• The effects of LIGO detector noise on a 15-dimensional Markov-chain Monte-Carlo analysis of gravitational-wave signals
• Combine Umbrella Sampling with Integrated Tempering Method for Efficient and Accurate Calculation of Free Energy Changes of Complex Energy Surface
• Adaptive ensemble simulations of biomolecules
• Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways
• Optimizing Replica Exchange Moves For Molecular Dynamics
• xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states
• Lymphotactin: how a protein can adopt two folds
• Phase equilibrium of liquid water and hexagonal ice from enhanced sampling molecular dynamics simulations
• Thermodynamics of Na_8 and Na_{20} clusters studied with ab-initio electronic structure methods
• Bayesian graph convolutional neural networks via tempered MCMC
• Spontaneous Domain Formation in Spherically-Confined Elastic Filaments
• Enhanced sampling in generalized ensemble with large gap of sampling parameter: case study in temperature space random walk
• Revisiting Bayesian Autoencoders with MCMC
• Monte Carlo Methods for Rough Free Energy Landscapes: Population Annealing and Parallel Tempering
• Generalized-Ensemble Simulations of the Human Parathyroid Hormone Fragment PTH(1-34)
• Efficient Irreversible Monte Carlo samplers
• Monte Carlo studies of the Ising square lattice with competing interactions
• Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
• Comparing parallel and simulated tempering enhanced sampling algorithms at phase transition regimes
• Infinite swapping replica exchange molecular dynamics leads to a simple simulation patch using mixture potentials
• RE-EDS Using GAFF Topologies: Application to Relative Hydration Free-Energy Calculations for Large Sets of Molecules
• Accelerating molecular dynamics simulations with population annealing
• Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer
• Metropolis simulations of Met-Enkephalin with solvent-accessible area parameterizations
• Adaptive Ensemble Biomolecular Simulations at Scale
• Refinement of molecular dynamics ensembles using experimental data and flexible forward models
• Protein simulations combining an all-atom force field with a Go term
• Point-like inclusion interactions in tubular membranes
• Simulated Tempering Method in the Infinite Switch Limit with Adaptive Weight Learning
• Backbone and Sidechain Ordering in a small Protein
• Influence of Bonded Interactions on Structural Phases of Flexible Polymers
• Side chain and backbone ordering in a polypeptide
• Combining Enhanced Sampling with Experiment Directed Simulation of the GYG peptide
• Order by disorder and phase transitions in a highly frustrated spin model on the triangular lattice
• Anisotropic frustrated Heisenberg model on the honeycomb lattice
• A comparative study of selected parallel tempering methods
• Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering
• Towards an optimal flow: Density-of-states-informed replica-exchange simulations
• Generalized-ensemble simulations of spin systems and protein systems
• An Efficient Simulation Protocol for Determining the Density of States: Combination of Replica-Exchange Wang-Landau Method and Multicanonical Replica-Exchange Method
• Comparison of two efficient methods for calculating partition functions
• Random template placement and prior information
• Exploring canyons in glassy energy landscapes using metadynamics
• MIST: A Simple and Efficient Molecular Dynamics Abstraction Library for Integrator Development
• Bayesian comparison of Post-Newtonian approximations of gravitational wave chirp signals
• Finite size scaling of the de Almeida-Thouless instability in random sparse networks
• Optimized Folding Simulations of Protein A
• A brief history of the introduction of generalized ensembles to Markov chain Monte Carlo simulations
• Single temperature for Monte Carlo optimization on complex landscapes
• Resolution Exchange with Tunneling for Enhanced Sampling of Protein Landscapes
• Topological floating phase in a spatially anisotropic frustrated Ising model
• Computational studies on magnetism and ferroelectricity
• Flat histogram method comparison on 2D Ising Model
• Calculation of molecular free energies in classical potentials
• Temperature Integration: an efficient procedure for calculation of free energy differences
• Estimating statistical distributions using an integral identity
• Integral equation study of effective attraction between like-charged particles mediated by cations: Comparison between IPY2 and HNC closures
• Quantum disordered ground state for the frustrated square lattice
• Closing the Evidence Gap: reddemcee, a Fast Adaptive Parallel Tempering Sampler
• Active Δ-learning with universal potentials for global structure optimization
• A short review on the maximum clique problem algorithms with classical, AI, and quantum methods
• Simulated tempering with irreversible Gibbs sampling techniques
• Parallel tempering as a mechanism for facilitating inference in hierarchical hidden Markov models
• Structural Comparison of Error Mitigation Methods for Ising Machines: Penalty-Spin Model versus Stacked Model