Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.About:
This article is published in Journal of Computational Physics.The article was published on 1977-03-01 and is currently open access. It has received 18394 citations till now. The article focuses on the topics: Generalized coordinates & Holonomic constraints.read more
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Anisotropic Intramolecular Backbone Dynamics of Ubiquitin Characterized by NMR Relaxation and MD Computer Simulation
TL;DR: Bremi et al. as discussed by the authors explored the anisotropy of rapid fluctuations of the peptide planes in ubiquitin by combined 15N and 13C nuclear spin relaxation measurements and molecular dynamics (MD) computer simulation.
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A short description of DL_POLY
TL;DR: This introduction provides an outline of the features of theDL_POLY, a general purpose molecular dynamics simulation package with in-built parallel algorithms, and the underlying methodology.
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Polarizable empirical force field for alkanes based on the classical Drude oscillator model.
TL;DR: The present alkane force field will act as the basis for the aliphatic moieties in an extensive empirical force field for biomolecules that includes the explicit treatment of electronic polarizability.
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Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle
TL;DR: Results indicate that the use of the atomic partial charges from the F‐HM further improves the accuracy of docked predictions for raloxifene to CYP3A4, and the new force field for the various heme states may aid the community for simulations of P450 enzymes and other heme‐containing enzymes.
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The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations.
TL;DR: The results from molecular dynamics simulations of Na(+) and K(+) hydration are reported based on a novel and rigorous strategy designed to overcome the challenges of QM/MM simulations of solvent molecules in the liquid phase.
References
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Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
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Improved simulation of liquid water by molecular dynamics
TL;DR: In this paper, a four-charge model for each molecule and a modification of the prior ''BNS'' interaction was proposed to improve the fidelity of the molecular dynamics simulation, leading to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x-ray scattering experiments.
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Molecular Dynamics Study of Liquid Water
TL;DR: In this paper, a sample of water, consisting of 216 rigid molecules at mass density 1 gm/cm3, has been simulated by computer using the molecular dynamics technique, subject to an effective pair potential that incorporates the principal structural effects of manybody interactions in real water.
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Molecular dynamics of liquid n-butane near its boiling point
TL;DR: The self-diffusion coefficient of n-butane is approximately 6.0 × 10−5 cm2/s and the corresponding velocity autocorrelation function displays practically no cage effect, differing markedly from argon and other simple fluids.
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Simulation of Diatomic Homonuclear Liquids
TL;DR: In this paper, the authors used the molecular-dynamic method to simulate a fluid of 500 rigid diatomic homo-nuclear molecules interacting by a double Lennard-Jones potential.