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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A Kirkwood-Buff derived force field for methanol and aqueous methanol solutions.
TL;DR: The force field was specifically designed to reproduce the experimental Kirkwood-Buff integrals as a function of meethanol mole fraction, thereby ensuring a reasonable description of the methanol cosolvent and water solvent activities.
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Brownian dynamics simulation of a lipid chain in a membrane bilayer
TL;DR: In this paper, a mean field derived from an extension of the Marcelja model was used to model the motional properties of a dipalmitoyl phosphatidylcholine bilayer.
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Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation
Michael Feig,Bernard Pettitt +1 more
TL;DR: Crystallographic results from a statistical analysis of hydration sites around DNA crystal structures compare very well with the simulation results, and more fully explain the observed B-->A transition at low humidity.
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New methodology for computer-aided modelling of biomolecular structure and dynamics. 1. Non-cyclic structures.
Alexey K. Mazur,Ruben Abagyan +1 more
TL;DR: A general methodology is proposed for the conformational modelling of biomolecular systems meant to be used in various investigations concerning the conformations and dynamics of biomacromolecules.
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A molecular dynamics simulation of crystalline alpha-cyclodextrin hexahydrate.
TL;DR: In this article, the structure of crystalline α-cyclodextrin (α-CD) hexahydrate, form I (C36H60O30·6H2O, space group P212121) is experimentally so well determined by X-ray and by neutron diffraction analyses that the positions of all the hydrogen atoms are available.
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.