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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Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States
TL;DR: By using feature selection algorithms to identify the most appropriate subset of relevant variables that describe a certain phenomenon, the high-dimensionality of QM/MM data can be reduced and used for further analysis with causal inference algorithms to establish unique cause-effect relationships.
Introduction to Molecular Dynamics Simulation
TL;DR: This paper presents a meta-analyses of the immune system’s response to TSPs and its applications in medicine and medicine-like settings.
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Generalized Born Model with a Simple, Robust Molecular Volume Correction
TL;DR: An earlier pairwiseGB model is extended by a simple analytic correction term that largely alleviates the problem by correctly describing the solvent-excluded volume of each pair of atoms and preserves the efficiency of the pairwise GB models while making them a better approximation to reality.
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Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations
TL;DR: In this article, four methods to compute the dielectric permittivity e of a liquid from molecular simulations are compared in the context of the simple point charge (SPC) water model.
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Restructuring the crystalline cellulose hydrogen bond network enhances its depolymerization rate
Shishir P. S. Chundawat,Giovanni Bellesia,Nirmal Uppugundla,Leonardo da Costa Sousa,Dahai Gao,Albert M. Cheh,Umesh P. Agarwal,Christopher M. Bianchetti,George N. Phillips,Paul Langan,Venkatesh Balan,Sandrasegaram Gnanakaran,Bruce E. Dale +12 more
TL;DR: How the synergistic activity of cellulases was enhanced by altering the hydrogen bond network within crystalline cellulose fibrils was demonstrated, which led to an enhancement in apparent cellulase activity and unique insight into the nature of cellulose recalcitrance.
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.