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, Monte Carlo Simulations, and Langevin Dynamics: A Computational Review
Eric Paquet,Herna L. Viktor +1 more
TL;DR: A computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.
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Simulations of the pressure and temperature unfolding of an α-helical peptide
TL;DR: In this paper, the reversible folding/unfolding equilibrium as a function of density and temperature of a solvated α-helical peptide was studied by molecular simulations.
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Molecular Dynamics Study of the Influence of Solid Interfaces on Poly(ethylene oxide) Structure and Dynamics
TL;DR: In this paper, a simulation of the interface between poly(ethylene oxide) and TiO2 has been performed at 423 K using a quantum chemistry-based force field, which revealed that the PEO density is significantly perturbed by TiO 2 surfaces, forming layers of highly dense polymer that persisted up to 15 A from the surface.
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Potential of mean force and pKa profile calculation for a lipid membrane-exposed arginine side chain.
TL;DR: Side chain analog and transmembrane helix models are employed to determine the free energy of an Arg side chain, as a function of protonation state, across a membrane, suggesting that although Arg side chains are ideally suited for carrying charge, the thermodynamics dictate that they must remain sequestered from the lipid bilayer environment.
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Flexible Structure of DNA: Ion Dependence of Minor-Groove Structure and Dynamics
TL;DR: Alternative models to explain the molecular basis for the minor groove narrowing of DNA results from direct, short-range interactions among DNA bases and any localization of monovalent cations in the groove does not affect the groove structure.
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.