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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The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration
TL;DR: The backbone dynamics of the pleckstrin homology (PH) domain from dynamin were studied by 15N NMR relaxation and steady state heteronuclear 15N [1H] nuclear Overhauser effect measurements, and by molecular dynamics simulations.
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A consensus view of protein dynamics.
Manuel Rueda,Carles Ferrer-Costa,Tim Meyer,Tim Meyer,Alberto Perez,Jordi Camps,Josep Lluís Gelpí,Josep Lluís Gelpí,Modesto Orozco +8 more
TL;DR: A detailed analysis of the massive database of trajectories allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution.
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Molecular Structure and Dynamics in Thin Water Films at the Silica and Graphite Surfaces
TL;DR: In this paper, the structure and dynamic properties of interfacial water at the graphite and silica solid surfaces were investigated using molecular dynamics simulations, and the effect of surface properties on the characteristics of inter-surface water was quantified by computing density profiles, radial distribution functions, surface density distributions, orientation order parameters, and residence and reorientation correlation functions.
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Polyunsaturated docosahexaenoic vs docosapentaenoic acid-differences in lipid matrix properties from the loss of one double bond.
TL;DR: It is proposed that the function of integral membrane proteins such as rhodopsin is sensitive to such a redistribution, and the loss of a single double bond from DHA to DPA results in a more even distribution of chain densities along the bilayer normal.
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Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers
Igor Vorobyov,Victor M. Anisimov,Shannon Greene,Richard M. Venable,Adam Moser,Richard W. Pastor,Alexander D. MacKerell +6 more
TL;DR: Empirical force field parameters consistent with the CHARMM additive and classical Drude based polarizable force fields are presented for linear and cyclic ethers and are shown to be in satisfactory agreement with both pure solvent and aqueous solvation properties.
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.