Molecular dynamics simulations at constant pressure and/or temperature
1980/02/15 by Hans C. Andersen, Hans Christian Andersen · 1 voice · 5,734 citations
Engineering · Materials Science · Mathematics · Physics and Astronomy · #Canonical ensemble #Classical mechanics #Computer science #Constant (computer programming) #Isobaric process #Isothermal process #Material Dynamics and Properties #Mathematics #Mechanics #Microcanonical ensemble #Molecular dynamics #Monte Carlo method #Phase Equilibria and Thermodynamics #Physics #Spectroscopy and Quantum Chemical Studies #Statistical physics #Statistics #Thermodynamics #Volume (thermodynamics)
paper · doi:10.1063/1.439486
published in The Journal of Chemical Physics 72(4), 2384-2393 (American Institute of Physics)
openalex publication_date 1980/02/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
Abstract
In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a particular simulation, and it is assumed that time averages of properties of the simulated fluid are equal to microcanonical ensemble averages of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temperature and/or pressure or under conditions in which the energy and volume of the fluid can fluctuate. This paper proposes and discusses three methods for performing molecular dynamics simulations under conditions of constant temperature and/or pressure, rather than constant energy and volume. For these three methods, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic–isobaric, canonical, and isothermal–isobaric ensembles. Each method is a way of describing the dynamics of a certain number of particles in a volume element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or density of the simulated volume element. The influence of the surroundings is taken into account without introducing unwanted surface effects. Examples of situations where these methods may be useful are discussed.
Citations
Cited by
- Polymorphic transitions in single crystals: A new molecular dynamics method
- Theoretical development in the realm of pentagonal 2D-materials
- A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model
- Constant pressure molecular dynamics for molecular systems
- A molecular dynamics method for simulations in the canonical ensemble
- Reversible work transition state theory: application to dissociative adsorption of hydrogen
- Understanding defect structures in metal additive manufacturing via molecular dynamics
- Dcdftbmd: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations
- Striking Impact of Solvent Polarity on the Strength of Hydrogen‐Bonded Complexes: A Nexus Between Theory and Experiment
- Accelerating Langevin Sampling with Birth-death
- Physical model for recognition tunneling
- Quasiharmonic lattice-dynamics and molecular-dynamics calculations for the Lennard-Jones solids
- Molecular insight into pyrolysis processes via reactive force field molecular dynamics: A state-of-the-art review
- Virus Assembly on a Membrane is Facilitated by Membrane Microdomains
- Towards an effective potential for the monomer, dimer, hexamer, solid, and liquid forms of hydrogen fluoride
- First principles interatomic potential for tungsten based on Gaussian process regression
- Enhanced Sampling Algorithms
- Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces
- Strain Effects on Electronic Properties of Cobalt-Based Coordination Nanosheets
- Markov models of molecular kinetics: Generation and validation
- Convenient Real-Time Monitoring of the Contamination of Surface Ion Trap
- Enhancing sampling in atomistic simulations of solid state materials for batteries: a focus on olivine NaFePO4
- Molecular dynamics at constant Cauchy stress
- Adaptive evolution of electron transfer pathways in Thermoanaerobacterium saccharolyticum
- Artificial Intelligence for Direct Prediction of Molecular Dynamics across Chemical Space
- Constant pressure molecular dynamics algorithms
- A molecular rotor driven by an electric field on graphene
- Computational modeling of biological nanopores
- CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations
- Canonical dynamics: Equilibrium phase-space distributions
- Influence of Thermostats on the Dynamics of the Helix-Coil Transition
- Statistical Properties of Current Noise Induced by Electron-Phonon Scattering in Metallic Carbon Nanotubes
- Frequency Dependence of Phonon-Induced Current Noise in ArmchairCarbon Nanotube
- Computationally guided genome rewiring of Escherichia coli and its application for nanopolyethylene terephthalate (PET) biodegradation and upcycling
- Phase Transitions Without Thermodynamic Limit,The Crucial Rôle of Possible and Impossible Fluctuations, The Treatment of Inhomogeneous Scenaria in the Microcanonical Ensemble
- Parallel athermal quasistatic deformation stepping of molecular systems
- The effect of solvents on crystal regeneration
- Correction of Density-Functional-Theory based polynomial interatomic potentials to reproduce experimental melting properties
- Classical and reactive molecular dynamics: Principles and applications in combustion and energy systems
- Atomistic theory for predicting the binary metallic glass formation
- Solvation of the Morpholinium Cation in Acetonitrile. Effect of an Anion
- Simulating phase transitions by means of quasi static state changes: the capabilities of the time dependent Van der Waals equation of state
- Molecular dynamic simulation of wet water vapour transport in porous medium
- Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics
- Bent surface free energy differences from simulation
- Electronic-Enthalpy Functional for Finite Systems Under Pressure
- Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides
- Machine learning model for efficient nonthermal tuning of the charge density wave in monolayer NbSe2
- Scalable molecular dynamics on CPU and GPU architectures with NAMD
- Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
- FlashMD: long-stride, universal prediction of molecular dynamics
- Improving protein expression, stability, and function with ProteinMPNN
- Hydrodynamic Correlations slow down Crystallization of Soft Colloids
- Melting of icosahedral gold nanoclusters from molecular dynamics simulations
- A Fully Anisotropic Formulation of Stochastic Cell Rescaling
- Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat
- Asymptotics of fixed point distributions for inexact Monte Carlo algorithms
- Extended Gibbs ensembles with flow
- A unified formulation of the constant temperature molecular dynamics methods
- Unjamming due to local perturbations in granular packings with and without gravity
- Expansion dynamics of Lennard-Jones systems
- Precision shooting: Sampling long transition pathways
- Hadron spectrum in QCD with valence Wilson fermions and dynamical staggered fermions at6g2=5.6
- Pushing the limits of unconstrained machine-learned interatomic potentials
- Multiscale investigation of chemical interference in proteins
- Large Language Models as AI Agents for Digital Atoms and Molecules: Catalyzing a New Era in Computational Biophysics
- Langevin Equation with Colored Noise for Constant-Temperature Molecular Dynamics Simulations
- Canonical ensembles from chaos
- Switching Hamiltonian Monte Carlo for sampling from mixture distributions
- Deriving GENERIC from a Generalized Fluctuation Symmetry
- Biological and synthetic membranes: What can be learned from a coarse-grained description?
- Transport coefficients of off-lattice mesoscale-hydrodynamics simulation techniques
- Molecular dynamics simulations of the dipolar-induced formation of magnetic nanochains and nanorings
- Molecular dynamics simulation of proteins under high pressure: Structure, function and thermodynamics
- Diffusion and viscosity in a supercooled polydisperse system
- Pair dynamics in a glass-forming binary mixture: Simulations and theory
- Cooling Rate Dependence of the Internal Structure of a Lennard-Jones Glass
- Application of the projection operator formalism to non-Hamiltonian dynamics
- DynamO: a free \cal O(N) general event‐driven molecular dynamics simulator
- Structure and stability of helices in square-well homopolymers
- Ab Initio Description of Optoelectronic Properties at Defective Interfaces in Solar Cells
- Diamond stabilization of ice multilayers at human body temperature
- G protein inactive and active forms investigated by simulation methods
- Metric-tensor flexible-cell algorithm for isothermal–isobaric molecular dynamics simulations
- Effective thermostat induced by coarse graining of simple point charge water
- Best Practices for Computing Transport Properties 1. Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]
- Thermal fluctuations in a lamellar phase of a binary amphiphile–solvent mixture: A molecular-dynamics study
- Unjamming of granular packings due to local perturbations: Stability and decay of displacements
- Optimized constant pressure stochastic dynamics
- SciCode-Verified: How Benchmark Defects Underestimated the Scientific-Coding Ability of Language Models
- Melting properties of a simple tight-binding model of transition metals. I. The region of half-filled d-band
- Distributed charge models of liquid methane and ethane for dielectric effects and solvation
- Sampling the isothermal-isobaric ensemble by Langevin dynamics
- The low temperature D + + H 2 → HD + H + reaction rate coefficient: a ring polymer molecular dynamics and quasi-classical trajectory study
- Hydrogen-bond relaxation dynamics: Resolving mysteries of water ice
- Systematic Coarse Graining: “Four Lessons and A Caveat” from Nonequilibrium Statistical Mechanics
- First-principles nonequilibrium deterministic equation of motion of a Brownian particle and microscopic viscous drag
- Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface
- Sparse identification of slow timescale dynamics
- Molecular-dynamics computer simulation of crystal growth and melting in Al 50 Ni 50
- Nonequilibrium Induced by Reservoirs: Physico‐Mathematical Models and Numerical Tests
- Diffusion of small light particles in a solvent of large massive molecules
- Molecular dynamics simulation using hard particles
- Predicting Crystal Structures: The Parrinello-Rahman Method Revisited
- A coarse-grained model for the elastic properties of cross linked short carbon nanotube/polymer composites
- Screened empirical bond-order potentials for Si-C
- An Efficient Integrator Scheme for Sampling the (Quantum) Isobaric-Isothermal Ensemble in (Path Integral) Molecular Dynamics Simulations
- Non-equilibrium by molecular dynamics: a dynamical approach
- Implementations of Nosé-Hoover and Nosé-Poincaré thermostats in mesoscopic dynamic simulations with the united-residue model of a polypeptide chain. [europepmc]
- Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. [europepmc]
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. [europepmc]
- Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. [europepmc]
- The C-terminal RNA binding motif of HuR is a multi-functional domain leading to HuR oligomerization and binding to U-rich RNA targets. [europepmc]
- Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal. [europepmc]
- A selectivity filter at the intracellular end of the acid-sensing ion channel pore. [europepmc]
- Mapping the Drude polarizable force field onto a multipole and induced dipole model. [europepmc]
- High-speed atomic force microscopy reveals structural dynamics of α-synuclein monomers and dimers. [europepmc]
- β-barrel Oligomers as Common Intermediates of Peptides Self-Assembling into Cross-β Aggregates. [europepmc]
- Inhibitor binding mode and allosteric regulation of Na + -glucose symporters. [europepmc]
- Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins. [europepmc]
- Amyloid Self-Assembly of hIAPP8-20 via the Accumulation of Helical Oligomers, α-Helix to β-Sheet Transition, and Formation of β-Barrel Intermediates. [europepmc]
- Best Practices for Foundations in Molecular Simulations [Article v1.0]. [europepmc]
- Molecular dynamics simulations in photosynthesis. [europepmc]
- Scalable molecular dynamics on CPU and GPU architectures with NAMD. [europepmc]
- Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. [europepmc]
- Tight docking of membranes before fusion represents a metastable state with unique properties. [europepmc]
- Carbon Nanodots from an In Silico Perspective. [europepmc]
- Applications of Molecular Dynamics Simulation in Protein Study. [europepmc]
- Newton-X Platform: New Software Developments for Surface Hopping and Nuclear Ensembles. [europepmc]
- The catalytic role of glutathione transferases in heterologous anthocyanin biosynthesis. [europepmc]
- Computational design of highly efficient thermostable MHET hydrolases and dual enzyme system for PET recycling. [europepmc]
- MLatom 3: A Platform for Machine Learning-Enhanced Computational Chemistry Simulations and Workflows. [europepmc]
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models. [europepmc]
Discussions
Related