Canonical sampling through velocity-rescaling

Abstract

We present a new molecular dynamics algorithm for sampling the canonical distribution. In this approach the velocities of all the particles are rescaled by a properly chosen random factor. The algorithm is formally justified and it is shown that, in spite of its stochastic nature, a quantity can still be defined that remains constant during the evolution. In numerical applications this quantity can be used to measure the accuracy of the sampling. We illustrate the properties of this new method on Lennard-Jones and TIP4P water models in the solid and liquid phases. Its performance is excellent and largely independent on the thermostat parameter also with regard to the dynamic properties.

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• Drug-induced activation of integrin alpha IIb beta 3 leads to minor localized structural changes
• Custom Flow in Molecular Dynamics
• Thermodynamics of site-specific small molecular ion interactions with DNA duplex: a molecular dynamics study
• Short pyridine-furan springs exhibit bistable dynamics of Duffing oscillators
• On the Role of Solvent in Hydrophobic Cavity-ligand Recognition Kinetics
• Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+
• Fine-Tuning Hydrophilic-Hydrophobic Balance in Stimuli-Responsive PEGPNIPAM Micelles for Controlled Drug Delivery
• Unified non-equilibrium simulation methodology for flow through nanoporous carbon membrane
• Bridging atomistic simulations and thermodynamic hydration models of aqueous electrolyte solutions
• Revealing the Low Temperature Phase of FAPbI${}_3$ using A Machine-Learned Potential
• Machine learning potentials for complex aqueous systems made simple
• CO2 packing polymorphism under confinement in cylindrical nanopores
• Non-equilibrium molecular dynamics and continuum modelling of transient freezing of atomistic solids
• Deterministic Covalent Organic Functionalization of Monolayer Graphene with 1,3-Dipolar Cycloaddition Via High Resolution Surface Engineering
• Three-phase equilibria of CO${}_2$ hydrate from computer simulation in presence of NaCl
• Linear Response Properties of Solvated Systems: A Computational Study
• Machine Learning Inference of Molecular Dipole Moment in Liquid Water
• The Equation of State of MH-III: a possible deep CH${}_4$ reservoir in Titan, Super-Titan exoplanets and moons
• Uncertainties in the Static Dielectric Constants computed from Molecular Dynamics Simulations
• Local stress and elastic properties of lipid membranes obtained from elastic energy variation
• Enhanced path sampling using subtrajectory Monte Carlo moves
• Enhanced Sampling for Free Energy Profiles with Post-Transition-State Bifurcations
• Metatensor and metatomic: foundational libraries for interoperable atomistic machine learning
• The Role of Pressure in Inverse Design for Assembly
• Exponential Scaling of Water Exchange Rates with Ion Interaction Strength from the Perspective of Dynamic Facilitation Theory
• A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals
• Proton-transfer spectroscopy beyond the normal-mode scenario
• Application of molecular simulations: Insight into liquid bridging and jetting phenomena
• Double layer in ionic liquids: capacitance vs temperature
• GPx4 is bound to peroxidized membranes by a hydrophobic anchor
• Weighted Active Space Protocol for Multireference Machine-Learned Potentials
• Unveiling the hidden reaction kinetic network of carbon dioxide in supercritical aqueous solutions
• Molecular dynamics simulation of the transformation of Fe-Co alloy by machine learning force field based on atomic cluster expansion
• Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
• Temperature measurement from perturbations
• Prediction of the univariant two-phase coexistence line of the tetrahydrofuran hydrate from computer simulation
• Sub-Nanometer Interfacial Hydrodynamics: The Interplay of Interfacial Viscosity and Surface Friction
• Antimalarial Artefenomel Inhibits Human SARS-CoV-2 Replication in Cells while Suppressing the Receptor ACE2
• The solid-state Li-ion conductor Li${}_7$TaO${}_6$: A combined computational and experimental study
• Camel back shaped Kirkwood-Buff Integrals
• Protein-like dynamical transition of hydrated polymer chains
• Efficient Generation of Stable Linear Machine-Learning Force Fields with Uncertainty-Aware Active Learning
• Improved precision scaling for simulating coupled quantum-classical dynamics
• Spontaneous Vibrations and Stochastic Resonance of Short Oligomeric Springs
• High throughput interactome determination via sulfur anomalous scattering
• Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators
• Thermal transport of confined water molecules in quasi-one-dimensional nanotubes
• Modified Poisson-Boltzmann theory for polyelectrolytes in monovalent salt solutions with finite-size ions
• Computing the thermal transport coefficient of neutral amorphous polymers using exact vibrational density of states: Comparison with experiments
• Structural and Dynamical Mechanisms of a Naturally Occurring Variant of the Human Prion Protein in Preventing Prion Conversion
• Understanding Interfacial Ice Premelting: Structure, Adhesion and Nucleation
• Disentangling enhanced diffusion and ballistic motion of excitons coupled to Bloch surface waves with molecular dynamics simulations
• First-principles thermal equation of state of fcc iridium
• Locating large flexible ligands on proteins
• Using metadynamics to build neural network potentials for reactive events: the case of urea decomposition in water
• The Challenge of Stochastic Størmer-Verlet Thermostats Generating Correct Statistics
• The irradiation of water ice by C${}^{+}$ ions in the cosmic environment
• Microsecond long atomistic simulation of supercooled water
• Water Boiling inside Carbon Nanotubes: Towards Efficient Drug Release
• Exciton diffusion in amorphous organic semiconductors: reducing simulation overheads with machine learning
• Optically induced anisotropy in time-resolved scattering: Imaging molecular scale structure and dynamics in disordered media with experiment and theory
• Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers
• Water cavitation results from the kinetic competition of bulk, surface and surface-defect nucleation events
• Molecular kinetics of solid and liquid CHCl${}_3$
• A multi-scale analysis of the CzrA transcription repressor highlights the allosteric changes induced by metal ion binding
• Melting curves of ice polymorphs in the vicinity of the liquid-liquid critical point
• Dynamic principle for ensemble control tools
• WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space
• Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments
• The central role of entropy in adiabatic ensembles and its application to phase transitions in the grand-isobaric adiabatic ensemble
• Insights into Dermal Permeation of Skin Oil Oxidation Products from Enhanced Sampling Molecular Dynamics Simulation
• Accurate Frozen Core Approximation for All-Electron Density-Functional Theory
• Bringing discrete-time Langevin splitting methods into agreement with thermodynamics
• Can molecular dynamics be used to simulate biomolecular recognition?
• Constant pH Simulation with FMM Electrostatics in GROMACS. (B) GPU Accelerated Hamiltonian Interpolation
• Computing chemical potentials of adsorbed or confined fluids
• Mixing of Metropolis-Adjusted Markov Chains via Couplings: The High Acceptance Regime
• Unraveling the interlayer and intralayer coupling in two-dimensional layered MoS${}_2$ by X-ray absorption spectroscopy and ab initio molecular dynamics simulations
• Correlating thermodynamics, morphology, mechanics and thermal transport in PMMA-PLA blends
• Hydrogen liquid-liquid transition from first principles and machine learning
• A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation
• Self-induced buckling in hollow microgels
• Resolution Exchange with Tunneling for Enhanced Sampling of Protein Landscapes
• Free Energy Landscape and Isomerization Rates of Au${}_4$ Clusters at Finite Temperature
• Electronic Structure of the Solvated Benzene Radical Anion
• Is it possible to overheat ice? The activated melting of TIP4P/Ice at solid-vapor coexistence
• A First-Principles Nonequilibrium Deterministic Equation of Motion of a Brownian Particle and Microscopic Viscous Drag
• Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model
• Multiple Topology Replica Exchange of Expanded Ensembles (MT-REXEE) for Multidimensional Alchemical Calculations
• Two-dimensional multiferroic NbPc COF with strong magnetoelectric coupling and room-temperature ferroelectricity
• Unveiling the Face-Dependent Ice Growth Kinetics: Insights from Molecular Dynamics on the Basal and Prism Surfaces
• Interaction between two polyelectrolytes in monovalent aqueous salt solutions
• Competitive Adsorption in Polymer Nanocomposites: The Molecular Weight and End-Group Effect Revealed by SANS and MD Simulations
• Acid Base Chemistry of Short Hydrogen Bonds: A Tale of Schrödinger's Cat in Glutamine-Derived Crystals
• Self-interaction and transport of solvated electrons in molten salts
• Self-consistent Quantum Linear Response with a Polarizable Embedding environment
• Simulation-Based Inference with Approximately Correct Parameters via Maximum Entropy
• Refinement of Thermostated Molecular Dynamics Using Backward Error Analysis
• Anisotropic and isotropic elasticity and thermal transport in monolayer C${}_{24}$ networks from machine-learning molecular dynamics
• Dynamical Heterogeneity in Supercooled Water and its Spectroscopic Fingerprints
• Polypeptide A9K at Nanoscale Carbon: Simulation Study
• Predictions of the interfacial free energy along the coexistence line from single-state calculations
• Exploring Conformational Landscapes Along Anharmonic Low-Frequency Vibrations
• Behavior of H-FABP-fatty acid complex in a protein crystal simulation
• Deriving effective electrode-ion interactions from free-energy profiles at electrochemical interfaces
• Usefulness of Higher Order of System-Size Correction for Diffusion Coefficients of Macromolecules: A Molecular Dynamics Study
• An atomic-scale perspective on individual thiol-terminated molecules anchored to single S vacancies in MoS${}_2$
• Mechanisms behind high CO2/CH4 selectivity using ZIF-8 metal organic frameworks with encapsulated ionic liquids: a computational study
• Path sampling challenges in large biomolecular systems: RETIS and REPPTIS for ABL-imatinib kinetics
• Relative Resolution: A Multipole Approximation at Appropriate Distances
• Surface-Induced Phase Transition During Coalescence of Au Nanoparticles: A Molecular Dynamics Simulation Study
• Water structuring at stacked graphene interfaces unveiled by machine-learning molecular dynamics
• Martini 3 application for the design of bistable nanomachines
• Efficient GPU-Accelerated Training of a Neuroevolution Potential with Analytical Gradients
• Regularized Fluctuating Lattice Boltzmann Model
• ${}^{27}\text{Al }$ NMR chemical shift of $\text{Al}(\text{OH}{)}_4^{-}$ from first principles. Assessment of error cancellation in NMR chemical shift computations in chemically distinct reference and targeted systems
• Velocity jump processes : an alternative to multi-timestep methods for faster and accurate molecular dynamics simulations
• Teaching oxidation states to neural networks
• Explaining classifiers to understand coarse-grained models
• Protein folding as a jamming transition
• Reaction Path Averaging: Characterizing the Structural Response of the DNA Double Helix to Electron Transfer
• Maintaining the equipartition theorem in small heterogeneous molecular dynamics ensembles
• Spontaneous synchronization of two bistable pyridine-furan nanosprings connected by an oligomeric bridge
• On the Role of Internal Degrees of Freedom in Structural Relaxation of Ring-Tail Structured Liquids Across Temperature Regimes
• Electrochemistry, Ion Adsorption and Dynamics in the Double Layer: A Study of NaCl(aq) on Graphite
• Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions
• Fast Sampling of Protein Conformational Dynamics
• Prediction of the three-phase coexistence line of the ethane hydrate from molecular simulation
• First Observation of Electron Transfer Mediated Decay in Aqueous Solutions: A Novel Probe of Ion Pairing
• Unraveling energy flow mechanisms in semiconductors by ultrafast spectroscopy: Germanium as a case study
• Ergostatting and Thermostatting at a Fixed Point
• Classification of interfacial water governed by water-polymer interactions in hydrated polymers: A molecular dynamics simulation study of ethylene-based and acrylate polymers
• Transport properties of monodisperse and bidisperse hard-sphere colloidal suspensions from multiparticle collision dynamics simulations
• MD Simulations of Charged Binary Mixtures Reveal a Generic Relation Between High- and Low-Temperature Behavior
• Implementation and Parallel Optimization of the Lees-Edwards Boundary Condition in ESPResSo++
• A Simplified Approach to Simulating Raman Spectra from Ab Initio Molecular Dynamics
• Estimating statistical distributions using an integral identity
• Dynamics and thermodynamics of Ibuprofen conformational isomerism at the crystal/solution interface
• The Effect of Hydration and Dynamics on the Mass Density of Single Proteins
• Local intermolecular structure, hydrogen bonding and related dynamics in the liquid cis/trans N-methylformamide mixture: A density functional theory based Born-Oppenheimer molecular dynamics study
• Local and Global Expansivity in Water
• Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats
• Imbibition of Oil in Dry and Prewetted Calcite Nanopores
• High-Throughput Computation of Anharmonic Low-Frequency Protein Vibrations
• Entropic bonding of the type 1 pilus from experiment and simulation
• Uncertainties in permittivities computed from molecular dynamics simulations and temperature correction of dielectric properties of condensed polar systems
• Efficient spectra from atomistic simulation: a generalized master equation study of the air-water interface
• clusttraj: A Solvent-Informed Clustering Tool for Molecular Modeling
• The Photochemical Birth of the Hydrated Electron in Liquid Water
• Ionic conductance oscillations in sub-nanometer pores probed by optoelectronic control
• Free energy calculations and unbiased dynamics reveal a continuous liquid-liquid transition in water no man's land
• Dynamics of Polyalkylfluorene Conjugated Polymers: Insights from Neutron Spectroscopy and Molecular Dynamics Simulations
• Coarse-graining bistability with the Martini force field
• Path collective variables without paths
• Elucidating Ion Capture and Transport Mechanisms of Preyssler Anions in Aqueous Solutions Using Biased MACE-Accelerated MD Simulations
• In search of the origin of long-time power-law decay in DNA solvation dynamics
• Thermal conductivities of monolayer graphene oxide from machine learning molecular dynamics simulations
• A Molecular-Continuum Multiscale Model for Inviscid Liquid-Vapor Flow with Sharp Interfaces
• Spectral signatures of excess-proton waiting and transfer-path dynamics in aqueous hydrochloric acid solutions
• Investigating finite-size effects in molecular dynamics simulations of ion diffusion, heat transport, and thermal motion in superionic materials
• Raman spectra of hydrocarbons under extreme conditions of pressure and temperature: a first-principles study
• Simple generic picture of toughness in solid polymer blends
• Stability and molecular pathways to the formation of spin defects in silicon carbide
• Reciprocal space temperature-dependent phonons method from ab-initio dynamics
• MARTINI-based Coarse-grained Model for Poly(alpha-peptoid)s
• A temperature-dependent implicit-solvent model of polyethylene glycol in aqueous solution
• A Residence-Time Approach for Determining Position-Dependent Diffusivities from Biased Molecular Simulations
• A computational approach to calculate the heat of transport of aqueous solutions
• Fluid flow at interfaces driven by thermal gradients
• Broad chemical transferability in structure-based coarse-graining
• Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot with Thermodynamics-Driven Machine Learning
• Non-Additive Ion Effects on the Coil-Globule Equilibrium of a Generic Polymer in Aqueous Salt Solutions
• Digital Surfactant
• Aqueous Solutions of Amino Acid Based Ionic Liquids. Dispersion and Structure
• Randomized Runge-Kutta-Nyström Methods for Unadjusted Hamiltonian and Kinetic Langevin Monte Carlo
• The Force Field for Amino Acid Based Ionic Liquids: Polar Residues
• Exploring electric field sensing for solid-state nanopores
• Nanoscale Carbon Greatly Enhances Mobility of a Highly Viscous Ionic Liquid
• Imidazolium Ionic Liquid Mediates Black Phosphorus Exfoliation while Preventing Phosphorene Decomposition
• Probing Glass Formation in Perylene Derivatives via Atomic Scale Simulations and Bayesian Regression
• A Denser Hydrogen Inferred from First-Principles Simulations Challenges Jupiter's Interior Models
• On the possibility of chiral symmetry breaking in liquid hydrogen peroxide
• Revealing the innate sub-nanometer porous structure of carbon nanomembranes with molecular dynamics simulations and highly charged ion spectroscopy
• Simulations of Crystal Nucleation from Solution at Constant Chemical Potential
• Water structure-forming capabilities are temperature shifted for different models
• (Meta-)stability and Core-Shell Dynamics of Gold Nanoclusters at Finite Temperature
• Anisotropy of the proton kinetic energy as a tool for capturing structural transition in nanoconfined H${}_2$O
• Low, high and very-high density forms of liquid water revealed by a medium-range order descriptor
• Engineering correlated Dirac fermions and flat bands on SiC with transition-metal adatom lattices
• Formation of abiogenic hydrocarbons in supercritical fluids under Earth's upper mantle conditions
• Assessing Position-Dependent Diffusion from Biased Simulations and Markov State Model Analysis
• Interfacial free energy of the structure II cyclopentane hydrate in cyclopentane liquid from the capillary wave fluctuation method
• Global free energy landscapes as a smoothly joined collection of local maps
• A Bayesian approach for extracting free energy profiles from cryo-electron microscopy experiments using a path collective variable
• Acetone as a Polar Cosolvent for Pyridinium-Based Ionic Liquids
• Wetting and Diffusion of Water on Pristine and Strained Phosphorene
• Influence of water models on water movement through AQP1
• Accelerated Atomistic Simulations of a Supramolecular Polymer in Water
• A patch that imparts unconditional stability to certain explicit integrators for SDEs
• Can Organic Ions Dissolve Fullerenes?
• Locking ssDNA in a Graphene-Terraces Nanopore and Steering Its Step-by-Step Transportation via Electric Trigger
• Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
• Electrotunable friction with ionic liquid lubricants: how important is the molecular structure of the ions?
• Transferable Coarse-Grained Model for Methacrylate-Based Copolymers
• Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models
• Quantifying surfactant adsorption at fluid interfaces by combining X-ray reflectivity and simulations
• Linking Theoretical and Simulation Approaches to Study Fluids in Nanoporous Media: Classical Molecular Dynamics and Density Functional Theory
• Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling
• Relaxing the aquaporin crystal structure in a membrane with surface vibrational spectroscopy
• Theoretical calculation of finite-temperature X-ray absorption fine structure: application to sodium K-edge in NaCl
• Strain-controlled thermoelectric properties of phosphorene hetero-bilayers
• Mode-selective ballistic pathway to a metastable electronic phase
• Spontaneous Directional Motion of Shaped Nanoparticle
• Anisotropic membrane curvature sensing by amphipathic peptides
• Improved capabilities of the TurboGAP code for radiation induced cascade simulations: an illustration with silicon
• Relative Resolution: A Hybrid Formalism for Fluid Mixtures
• A Reversible Unwrapping Algorithm for Constant Pressure Molecular Dynamics Simulations
• Tuning the Transdermal Transport by Application of External Continuous Electric Field: A Molecular Dynamics Coarse-Grained Study
• Computing rates and understanding unbinding mechanism in host-guest systems
• Memory Control of Ice Growth During Non-Equilibrium Freezing of Water
• Does Like Dissolves Like Rule Hold for Fullerene and Ionic Liquids?
• Characterizing Solvent Density Fluctuations in Dynamical Observation Volumes
• Effects of skewing collision cells on transport properties in multiparticle collision dynamics simulations
• Inherent fluctuation-mediated equivalent force drives directional motions of nanoscale asymmetric particles -- Surf-riding of asymmetric molecules in thermal fluctuations