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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Enhanced Concentration of Polarizable Anions at the Liquid Water Surface: SHG Spectroscopy and MD Simulations of Sodium Thiocyanide
TL;DR: In this paper, a combined experimental and theoretical investigation of the liquid/air interface of aqueous sodium thiocyanide at varying salt concentrations is presented, which is in accord with molecular dynamics simulations in slab geometry, which predict an appreciable surface enhancement of SCN-.
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Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide
TL;DR: The kinetics of a conformational transition in a blocked alanine is computed and shown to be accurate, more efficient than straightforward molecular dynamics by a factor of about 9, and nonexponential.
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A molecular dynamics study of the structure of water around the ions Li+, Na+, K+, Ca++, Ni++ and Cl-
TL;DR: In this article, a molecular dynamics study of the structure of water around Li+, Na+, K+, Ca++, Ni++ and Cl- ions is presented, where the positions of the peaks associated with the coordination shells, the ion-water geometries, and the coordination numbers are in satisfactory agreement.
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Structural Determinants of MscL Gating Studied by Molecular Dynamics Simulations
TL;DR: The gating process was investigated through simulations of the bare protein under conditions of constant surface tension and under a range of conditions, the transmembrane helices flattened as the pore widened.
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A new coarse-grained model for water: the importance of electrostatic interactions.
Zhe Wu,Qiang Cui,Arun Yethiraj +2 more
TL;DR: This big multipole water (BMW) model represents a qualitative improvement over existing CG water models; for example, it reproduces the dipole potential in membrane-water interface when compared to experiment, with modest additional computational cost as compared to the popular MARTINI CG model.
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.