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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Exploring multiple timescale motions in protein GB3 using accelerated molecular dynamics and NMR spectroscopy.
TL;DR: The results provide rare insight into the complex hierarchy of dynamics present in GB3 and allow us to develop a model of the conformational landscape native to the protein, appearing as a steep sided potential well whose flat bottom comprises multiple similar but discrete conformational substates.
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Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics
TL;DR: A new formula expressing the components of the mean force in terms of a conditional expectation which can be computed by Blue Moon sampling is given, which generalizes to the vectorial case a formula first derived by Ruiz-Montero et al.
Biological and medical physics, biomedical engineering
TL;DR: The Biological and Medical Physics, Biomedical Engineering Series is intended to be comprehensive, covering a broad range of topics important to the study of the physical, chemical and biological sciences.
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Martini Coarse-Grained Force Field: Extension to RNA
TL;DR: The coarse-grain Martini force field is extended to include RNA, and the tertiary structure of RNA is constrained using an elastic network, which opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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Passive Transport of C60 Fullerenes through a Lipid Membrane: A Molecular Dynamics Simulation Study
TL;DR: Simulations reveal that the free energy decreases as the fullerene passes from the aqueous phase, through the head group layer and into the hydrophobic core of the membrane, indicating that the large permeability of fullerenes through lipid membranes is a result of their unique interaction with their surrounding medium.
References
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Journal ArticleDOI
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.