Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

Abstract

We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In collective-variable biasing, we first discuss methods stemming from thermodynamic integration that use mean force biasing, including the adaptive biasing force algorithm and temperature acceleration. We then turn to methods that use bias potentials, including umbrella sampling and metadynamics. We next consider parallel tempering and replica-exchange methods. We conclude with a brief presentation of some combination methods.

Accepted for publication on Entropy

References in corpus (9)

• PLUMED 2: New feathers for an old bird
• Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
• PLUMED: a portable plugin for free-energy calculations with molecular dynamics
• Equilibrium free energies from non-equilibrium metadynamics
• Metadynamics with adaptive Gaussians
• Hamiltonian replica-exchange in GROMACS: a flexible implementation
• Single-Sweep Methods for Free Energy Calculations
• A self-learning algorithm for biased molecular dynamics
• RNA/peptide binding driven by electrostatics -- Insight from bi-directional pulling simulations

Cited by in corpus (38)

• Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations
• Molecular enhanced sampling with autoencoders: On-the-fly collective variable discovery and accelerated free energy landscape exploration
• Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies
• A Unified Approach to Enhanced Sampling
• iMapD: intrinsic Map Dynamics exploration for uncharted effective free energy landscapes
• Folding of guanine quadruplex molecules -- funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies
• Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering
• Exploring High Dimensional Free Energy Landscapes: Temperature Accelerated Sliced Sampling
• Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis
• Path Similarity Analysis: a Method for Quantifying Macromolecular Pathways
• From data to noise to data: mixing physics across temperatures with generative artificial intelligence
• Enhanced Sampling in the Age of Machine Learning: Algorithms and Applications
• Multiscale reweighted stochastic embedding (MRSE): Deep learning of collective variables for enhanced sampling
• Making the best of a bad situation: a multiscale approach to free energy calculation
• Hairpins Participating in Folding of Human Telomeric Sequence Quadruplexes Studied by Standard and T-REMD Simulations
• Pre-training of Equivariant Graph Matching Networks with Conformation Flexibility for Drug Binding
• Accurate multiple time step in biased molecular simulations
• ATP dependent NS3 helicase interaction with RNA: insights from molecular simulations
• Reaction Coordinates for Conformational Transitions using Linear Discriminant Analysis on Positions
• CO2 packing polymorphism under pressure: mechanism and thermodynamics of the I-III polymorphic transition
• Machine Learning of consistent thermodynamic models using automatic differentiation
• Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
• From Free-Energy Profiles to Activation Free Energies
• TimeSOAP: Tracking high-dimensional fluctuations in complex molecular systems via time-variations of SOAP spectra
• PySAGES: flexible, advanced sampling methods accelerated with GPUs
• Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
• Manifold Learning in Atomistic Simulations: A Conceptual Review
• Longtime convergence of the Temperature-Accelerated Molecular Dynamics Method
• Self-assembly of a model supramolecular polymer studied by replica exchange with solute tempering
• Jarzynski's equality, fluctuation theorems, and variance reduction: Mathematical analysis and numerical algorithms
• Magnetic Interactions between Nanoscale Domains in Correlated Liquids
• Metashooting: A Novel Tool for Free Energy Reconstruction from Polymorphic Phase Transition Mechanisms
• Properties of low-dimensional collective variables in the molecular dynamics of biopolymers
• Determination of protein structural ensembles using cryo-electron microscopy
• Automated Prediction of Thermodynamic Properties via Bayesian Free-Energy Reconstruction from Molecular Dynamics
• On the construction of general cubature formula by flat extensions
• Improving the Exploration of High Dimensional Free Energy Landscape by a Combination of Temperature Accelerated Sliced Sampling and Parallel Biasing
• Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann -- All Atom Molecular Dynamics Coupling