Constant pressure molecular dynamics for molecular systems

1983/12/10 by Shuichi Nosé, Shūichi Nosé, M.L. Klein +1 · 3,355 citations
Chemistry · Earth and Planetary Sciences · Mathematics · Physics and Astronomy · #Advanced Chemical Physics Studies #Charge (physics) #Chemistry #Computational chemistry #Computer science #Constant (computer programming) #Constraint (computer-aided design) #Crystallography and molecular interactions #High-pressure geophysics and materials #Materials science #Mathematics #Molecular dynamics #Oscillation (cell signaling) #Physics #Quantum mechanics #Range (aeronautics) #Statistical physics #Thermodynamics

paper · doi:10.1080/00268978300102851

published in Molecular Physics 50(5), 1055-1076 (Taylor & Francis)

openalex publication_date 1983/12/10 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06

Abstract

Technical aspects of the constant pressure molecular dynamics (MD) method proposed by Andersen and extended by Parrinello and Rahman to allow changes in the shape of the MD cell are discussed. The new MD method is extended to treat molecular systems and to include long range charge-charge interactions. Results on the conservation laws, the frequency of oscillation of the MD cell, and the equations which constrain the shape of the MD cell are also given. An additional constraint is introduced to stop the superfluous MD cell rotation which would otherwise complicate the analysis of crystal structures. The method is illustrated by examining the behaviour of solid nitrogen at high pressure.

Citations

• Polymorphic transitions in single crystals: A new molecular dynamics method
• Molecular dynamics simulations at constant pressure and/or temperature

Cited by

• A molecular dynamics method for simulations in the canonical ensemble
• Bat genomes illuminate adaptations to viral tolerance and disease resistance
• Pressure induced amorphization of materials
• Hydrogen bonding blues: Vibrational spectroscopy of the TIP3P water model
• За кулисами русско-японских переговоров 1906-1907 гг. : дипломатия Мотоно Итиро
• GROMACS: Fast, flexible, and free
• New class of compounds - variators - are reprogramming substrate specificity of H4K12Ac, H4K16Ac and H4K20Ac epigenetic marks reading bromodomain of BPTF protein
• Understanding the characteristic behaviour of the wild-type and mutant structure of FLT3 protein by computational methods
• The SARS-CoV-2 Spike Protein is vulnerable to moderate electric fields
• Transient dynamics of flavonoid metabolons tune chalcone synthase specificity
• Mass spectrometric assays monitoring the deubiquitinase activity of the SARS-CoV-2 papain-like protease inform on the basis of substrate selectivity and have utility for substrate identification
• Molecular dynamics at constant Cauchy stress
• Harnessing the power of anti-amyloidogenic polyglutamine binding peptide 1: A computational and biophysical approach to antimicrobial prediction
• Tuning solvent strength can fractionate PVC into ultra-low molecular weight material with low dispersity
• Constant pressure molecular dynamics algorithms
• Molecular dynamics simulation study on the binding mechanism between carbon nanotubes and RNA-dependent RNA polymerase
• Response Theory for Static and Dynamic Solvation of Ionic and Dipolar Solutes in Water
• Thermoresponsive copolymer microgels synthesized via single-step precipitation polymerization: random or block structure?
• Stick of Sticks: Structural Features of the Amyloidogenic Peptide-DNA Complex
• Complexation of siRNA with Galactose-Functionalized Dendrimers: PAMAM vs PETIM
• Abundancia relativa y distribución de aves marinas frente a la costa peruana y su relación con la anchoveta. Crucero BIC Humboldt 9803-05 de Tumbes a Tacna
• Effect of Hydrostatic Pressure on the g Tensor and Hyperfine Coupling Constants of the Nitroxide Radical Characterized by Ab Initio Calculations
• New class of compounds - variators - are reprogramming substrate specificity of H3K4me3 epigenetic marks reading PHD domain of BPTF protein
• Competitive Adsorption in Polymer Nanocomposites: The Molecular Weight and End-Group Effect Revealed by SANS and MD Simulations
• Statistical Mechanics: Theory and Molecular Simulation
• Comparison of water models for structure prediction
• Separation of furfuryl alcohol from water using hydrophobic deep eutectic solvents
• Energetics and Kinetics of Membrane Permeation of Photoresists for Bioprinting
• Hamiltonian replica exchange augmented with diffusion-based generative models and importance sampling to assess biomolecular conformational basins and barriers
• A unified formulation of the constant temperature molecular dynamics methods
• Toward an anisotropic atom–atom model for the crystalline phases of the molecular S8 compound
• Reduction of the glass transition temperature in polymer films: A molecular-dynamics study
• Adding salt to an aqueous solution of t-butanol: Is hydrophobic association enhanced or reduced?
• Search for structural differences in spike glycoprotein variants of SARS-CoV-2: Infrared Spectroscopy, Circular Dichroism and Computational Analysis
• Scaling behaviour for the water transport in nanoconfined geometries
• Adduct of the blistering warfare agent sesquimustard with human serum albumin and its mass spectrometric identification for biomedical verification of exposure
• Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
• Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece
• Test of a simple and flexible molecule model for α-, β-, and γ-S8 crystals
• El tránsito de Venus: astronomía en la calle
• Predicting Crystal Structures: The Parrinello-Rahman Method Revisited
• An Efficient Integrator Scheme for Sampling the (Quantum) Isobaric-Isothermal Ensemble in (Path Integral) Molecular Dynamics Simulations
• Low-temperature and high-pressure induced swelling of a hydrophobic polymer-chain in aqueous solution
• Progress and challenges in the automated construction of Markov state models for full protein systems. [europepmc]
• Electrostatic frequency shifts in amide I vibrational spectra: direct parameterization against experiment. [europepmc]
• Antimicrobial peptides design by evolutionary multiobjective optimization. [europepmc]
• Time-resolved force distribution analysis. [europepmc]
• CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. [europepmc]
• Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors. [europepmc]
• Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling. [europepmc]
• Activation of Toll-like receptors nucleates assembly of the MyDDosome signaling hub. [europepmc]
• Structural basis of actin monomer re-charging by cyclase-associated protein. [europepmc]
• The architecture of the OmpC-MlaA complex sheds light on the maintenance of outer membrane lipid asymmetry in Escherichia coli . [europepmc]
• Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides. [europepmc]
• Outward open conformation of a Major Facilitator Superfamily multidrug/H + antiporter provides insights into switching mechanism. [europepmc]
• Structure of the human ClC-1 chloride channel. [europepmc]
• Lysosomal integral membrane protein-2 (LIMP-2/SCARB2) is involved in lysosomal cholesterol export. [europepmc]
• Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane. [europepmc]
• Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. [europepmc]
• Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane. [europepmc]
• On the molecular origins of the ferroelectric splay nematic phase. [europepmc]
• The antidepressant drug vilazodone is an allosteric inhibitor of the serotonin transporter. [europepmc]
• The importance of intramolecular hydrogen bonds on the translocation of the small drug piracetam through a lipid bilayer. [europepmc]
• Molecular mechanism of the skin permeation enhancing effect of ethanol: a molecular dynamics study. [europepmc]
• Potential Autoimmunity Resulting from Molecular Mimicry between SARS-CoV-2 Spike and Human Proteins. [europepmc]
• Structure of SARS-CoV-2 membrane protein essential for virus assembly. [europepmc]
• Structure of SARS-CoV-2 M protein in lipid nanodiscs. [europepmc]
• Conformational changes in the human Cx43/GJA1 gap junction channel visualized using cryo-EM. [europepmc]

Related

• The constant-pressure molecular dynamics for finite systems and its applications
• Constant pressure molecular dynamics algorithms
• An algorithm for very high pressure molecular dynamics simulations
• Molecular dynamics simulations at constant pressure and/or temperature
• Determination of Forces from a Potential in Molecular Dynamics