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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Molecular dynamics simulations of the unfolding of apomyoglobin in water
TL;DR: Detailed analyses of the final structures and the unfolding pathways at high temperature clearly show that the most stable alpha-helical regions are those in contact with other helices.
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Disorder in the pseudohexagonal rotator phase of n-alkanes: molecular-dynamics calculations for tricosane
TL;DR: In this article, molecular-dynamics calculations for a flexible-chain model have been used to study two, solid, bilayer phases of the n-alkane tricosane (C23H48).
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Hydration and DNA Recognition by Homeodomains
TL;DR: A 2-nanosecond molecular dynamics simulation of an Antennapedia homeodomain-DNA complex in explicit solvent water at ambient temperature and pressure was performed to supplement experimental nuclear magnetic resonance (NMR) data on the structure and dynamics of this complex.
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Evaluating the potency of HIV‐1 protease drugs to combat resistance
TL;DR: This study identified residues that have significant contributions to binding with six substrates using molecular dynamics simulations and Molecular Mechanics Generalized Born Surface Area calculations and defined an empirical parameter called free energy/variability (FV) value, which was shown to identify single resistant mutations with an accuracy of 88%.
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Protein molecular dynamics with the generalized Born/ACE solvent model.
TL;DR: The generalized Born (GB) solvent polarization model as implemented in the analytical ACE potential is used to perform molecular dynamics simulations of two small, homologous proteins: the immunoglobulin‐binding domain of streptococcal protein G and the Ras binding domain of Raf.
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.