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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Ion permeation mechanism of the potassium channel
TL;DR: Results from molecular dynamics free energy perturbation calculations that both establish the nature of the multiple ion conduction mechanism and yield the correct ion selectivity of the K+ channel are reported.
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Molecular dynamics simulation of rigid molecules
TL;DR: A review of the method of constraints, devised to carry out Molecular Dynamics simulations of complex molecular systems with some internal degrees of freedom frozen, in terms of atomic Cartesian coordinates, and deriving the statistical-mechanical formalism for these systems.
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Mechanism of Ion Transport in Amorphous Poly(ethylene oxide)/LiTFSI from Molecular Dynamics Simulations
Oleg Borodin,Grant D. Smith +1 more
TL;DR: In this paper, the mechanisms of lithium cation (Li+) and bis(trifluoromethane)sulfonamide anion (TFSI-) transport in poly(ethylene oxide) (PEO, Mw = 2380) melts were examined using molecular dynamics simulations over a wide range of salt concentrations and temperatures.
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Unified molecular picture of the surfaces of aqueous acid, base, and salt solutions.
Martin Mucha,Tomaso Frigato,Lori M. Levering,Heather C. Allen,Douglas J. Tobias,Liem X. Dang,Pavel Jungwirth +6 more
TL;DR: A unified and consistent view of the structure of the air/solution interface of aqueous electrolytes containing monovalent inorganic ions is presented, showing that both cations and anions exhibit enhanced concentrations at the surface and, consequently, these acids (unlike bases and salts) reduce the surface tension of water.
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Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies.
TL;DR: To test and validate the Automated force field Topology Builder and Repository (ATB), the hydration free enthalpies for a set of 214 drug-like molecules, including 47 molecules that form part of the SAMPL4 challenge have been estimated using thermodynamic integration and compared to experiment.
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.