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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Wettability of kaolinite (001) surfaces — Molecular dynamic study
TL;DR: In this paper, the authors investigated the hydrophilic properties of two (001) basal kaolinite surfaces (tetrahedral and octahedral) by means of force-field molecular dynamics simulation.
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Single-molecule pulling simulations can discern active from inactive enzyme inhibitors.
TL;DR: An in silico approach to study molecular interactions and to compare the binding characteristics of ligand analogues was devised, hypothesized an interaction model that both explained the biological activity of known ligands, and provided insight into designing novel enzyme inhibitors.
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Helical ice-sheets inside carbon nanotubes in the physiological condition
TL;DR: In this article, molecular dynamics simulations were performed on nanotube segments of various diameters submerged in water, and it was shown that water molecules can exist inside the nanotubes segments, and that the water molecules inside the tubes tend to organize themselves into a highly hydrogen-bonded network, i.e., solid-like wrapped-around ice sheets.
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Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding.
TL;DR: The GROMOS 54A7 force field developed to improve the stability of α-helical structures in proteins can thus be safely used in simulations of β-peptides.
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Computational Studies of the Mechanism for Proton and Hydride Transfer in Liver Alcohol Dehydrogenase
TL;DR: In this paper, computational studies were conducted to elucidate the mechanism of the oxidation of benzyl alcohol by liver alcohol dehydrogenase (LADH) using a 148-atom model of the active site.
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.