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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Zinc binding in proteins and solution: A simple but accurate nonbonded representation
Roland H. Stote,Martin Karplus +1 more
TL;DR: It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc‐containing systems.
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Dielectric relaxation in water. Computer simulations with the TIP4P potential
TL;DR: In this paper, extensive molecular dynamics simulations with the empirical TIP4P effective pair potential are compared with the experimental data for water as well as with the results reported previously for the MCY a b i n i t i o model.
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Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water
TL;DR: In this paper, statistical ensembles for simulating liquid interfaces at constant pressure and/or surface tension are examined, and equations of motion for molecular dynamics are obtained by various extensions of the Andersen extended system approach.
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Molecular dynamics simulation of nucleic acids: successes, limitations, and promise.
TL;DR: An overview of the experiences, some cautionary notes, and recommendations for further study in molecular dynamics simulation of nucleic acids are provided.
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Molecular Dynamics of the KcsA K+ Channel in a Bilayer Membrane
TL;DR: The mechanical response of the channel structure at distances as large as 10-20 A from the ions in the selectivity filter appears to play an important role in the concerted transition.
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.