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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Molecular dynamics studies of the liquid-vapor interface of water
TL;DR: In this paper, the results of molecular dynamics simulations of the liquid-vapor interface of water were studied and the density profile of the interfacial transition region between liquid and vapor is monotone with a 10% to 90% width of 3.45 A, in good agreement with the value determined from x-ray reflectance measurements, namely 3.30 A.
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GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.
Chigusa Kobayashi,Jaewoon Jung,Yasuhiro Matsunaga,Takaharu Mori,Tadashi Ando,Koichi Tamura,Motoshi Kamiya,Yuji Sugita +7 more
TL;DR: The string method and replica‐exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free‐ energy pathway and obtaining free‐energy profiles for conformational changes of a macromolecule.
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Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling.
TL;DR: The results complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: approximately 30 ps (hydroxyl groups), approximately 1 ns (free lactol group, free hydroxymethyl groups), and approximately 10 ns to 2 micros (ring conformation, glycosidic dihedral angles phi and psi).
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Nucleation of Methane Hydrates at Moderate Subcooling by Molecular Dynamics Simulations
TL;DR: In this article, a series of nanoscale molecular dynamics simulations of supersaturated water-methane mixtures was performed and it was shown that the order of the crystalline structure increases by decreasing subcooling.
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Enveloping distribution sampling: a method to calculate free energy differences from a single simulation.
TL;DR: The authors present a method to calculate free energy differences between two states A and B "on the fly" from a single molecular dynamics simulation of a reference state R using Hamiltonian replica-exchange molecular dynamics of the reference state.
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.