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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Structure Calculation of Biological Macromolecules From NMR Data
TL;DR: The introduction of nuclear magnetic resonance spectroscopy as a technique for protein structure determination has made it possible to obtain structures with comparable accuracy also in a solution environment that is much closer to the natural situation in a living being than the single crystals required for protein crystallography.
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Internal Coordinates for Molecular Dynamics and Minimization in Structure Determination and Refinement
TL;DR: A software module is presented which allows one to efficiently perform molecular dynamics and local minimization calculations in internal coordinates when incorporated into a molecular dynamics package and provides superior torsion-angle dynamics functionality relative to the native X-PLOR implementation.
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Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.
TL;DR: By formulating TAMD in a manner that is closer to the original AFED approach, including the generalized Gaussian moment thermostat (GGMT) and multiple time-scale integration, multidimensional free energy surfaces for complex systems can be generated directly from the probability distribution function of the extended phase-space variables.
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Force fields and molecular dynamics simulations
TL;DR: The basic concepts needed to understand the Molecular Dynamics technique are reviewed, including a general overview of the main algorithms employed to integrate the equations of motion, compute the long-range forces, work on different thermodynamic ensembles, or reduce the computational time.
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New tacrine-huperzine A hybrids (huprines): highly potent tight-binding acetylcholinesterase inhibitors of interest for the treatment of Alzheimer's disease.
Pelayo Camps,El Achab R,Jordi Morral,Diego Muñoz-Torrero,Albert Badia,Josep-Eladi Baños,Nuria M. Vivas,Xavier Barril,Modesto Orozco,Francisco J. Luque +9 more
TL;DR: Molecular modeling simulations of the AChE-inhibitor complex provided a basis to explain the differences in inhibitory activity of these compounds and supported the tight-binding character of compounds (-)-20 and (-)-30 and showed their ability to cross the blood-brain barrier.
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.