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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Pair correlations in an NaCl-SPC water model simulations versus extended RISM computations.
TL;DR: In this article, the ten pair correlation functions characterizing the equilibrium structure of a simple electrolyte such as NaCl-water were tested against molecular dynamics, constrained dynamics and Monte Carlo simulations employing Ewald and reaction field schemes for a high-temperature, highpressure thermodynamic state.
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Simple reversible molecular dynamics algorithms for Nosé-Hoover chain dynamics
Seogjoo Jang,Gregory A. Voth +1 more
TL;DR: In this paper, reversible algorithms for NHC dynamics are developed by simple extensions of Verlet-type algorithms: leap frog, position Verlet, and velocity Verlet for one-dimensional harmonic oscillators.
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Molecular Simulation of the Diffusion of Uranyl Carbonate Species in Aqueous Solution
TL;DR: In this article, potential-based molecular dynamics simulations of aqueous uranyl carbonate species (MxUO2(CO3)y2+2x−2y with Mg, Ca, or Sr) were carried out to gain molecular-level insight into the hydration properties of these species.
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Conformational transitions of the serotonin 5-HT3receptor.
Lucie Polovinkin,Ghérici Hassaine,Jonathan Perot,Emmanuelle Neumann,Anders A. Jensen,Solène N Lefebvre,Pierre-Jean Corringer,Jacques Neyton,Christophe Chipot,Christophe Chipot,François Dehez,François Dehez,Guy Schoehn,Hugues Nury +13 more
TL;DR: Cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator are reported, deepening understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
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Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.
TL;DR: The need for careful parametrization of coarse-grained force fields is illustrated and the utility of atomistic molecular dynamics for providing quantitative thermodynamic and mechanistic analysis of protein-lipid interactions is demonstrated.
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.