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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Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments
TL;DR: In this paper, a comparison of six popular force fields, including the AMBER, CHARMM, GROMOS, and OPLS models, is performed using 20 ns long molecular-dynamics simulations.
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Computational searching and mutagenesis suggest a structure for the pentameric transmembrane domain of phospholamban.
TL;DR: It is shown that for phospholamban, the global search can be further simplified by reducing the problem to two- body, rather than many-body, interactions, and this method of a constrained global search combined with experimental mutagenesis data yields a three-dimensional structure.
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Simulated surface tensions of common water models.
Feng Chen,Paul E. Smith +1 more
TL;DR: It is shown that a variety of simulation conditions can affect the final surface tension values and the SPC/E and TIP6P models provide the best agreement with experiment.
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Simulation of adsorption of DNA on carbon nanotubes.
Xiongce Zhao,J.K. Johnson +1 more
TL;DR: Molecular dynamics simulations of DNA adsorption on a single-walled carbon nanotube (SWNT) in an aqueous environment show that DNA binds to the external surface of an uncharged or positively charged SWNT on a time scale of a few hundred picoseconds.
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Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
TL;DR: State-of-the-art atomistic simulation is used to explore the packing defect structure of curved membranes, and the effect of this structure on the folding of H0, suggesting H0 folding is a cooperative process in which the folding peptide changes the defect structure relative to an unperturbed membrane.
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.