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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Studying the Stability of a Helical β‐Heptapeptide by Molecular Dynamics Simulations
TL;DR: In this paper, the 3-helical conformation of 1 was shown to be so stable that it was restored spontaneously within 400 ps after unfolding helical structures after molecular dynamics simulations.
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Determination of a transition state at atomic resolution from protein engineering data.
TL;DR: The combination of low-resolution C(alpha) results with all-atom molecular dynamics simulations provides a powerful and general method for determining the nature of TSEs from protein engineering data.
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Sequence-dependent DNA deformability studied using molecular dynamics simulations
TL;DR: The results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein–DNA recognition.
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Effectiveness of the Young-Laplace equation at nanoscale.
Hailong Liu,Guoxin Cao +1 more
TL;DR: Using molecular dynamics simulations, a new approach based on the behavior of pressurized water out of a nanopore in a flat plate is developed to calculate the relationship between the water surface curvature and the pressure difference across water surface, and it is found that this relationship will be effective for different pore size, temperature, and even for electrolyte solutions.
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Molecular modeling of the enantioselectivity in lipase-catalyzed transesterification reactions.
TL;DR: Two strategies based on the use of subsets for calculating the enantioselectivity in lipase-catalyzed transesterifications using the CHARMM force field were investigated and molecular dynamics was used in the search for low energy conformations.
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.