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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Structures of Cl-(H2O)n and F -(H2O)n (n=2,3,..., 15) clusters. Molecular dynamics computer simulations
Lalith Perera,Max L. Berkowitz +1 more
TL;DR: In this article, the authors have performed molecular dynamics calculations on Cl−(H2O)n and F −(H 2 O)n (n=2,3,...,15) clusters and showed that the F− ion is solvated in these clusters, while Cl− remains attached to the water in the clusters.
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An integrate-over-temperature approach for enhanced sampling.
TL;DR: A simple method is introduced to achieve efficient random walking in the energy space in molecular dynamics simulations which thus enhances the sampling over a large energy range.
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Sitting at the Edge: How Biomolecules use Hydrophobicity to Tune Their Interactions and Function
Amish J. Patel,Patrick Varilly,Sumanth N. Jamadagni,Michael F. Hagan,David Chandler,Shekhar Garde +5 more
TL;DR: Molecular simulations with specialized sampling techniques are used to show that water density fluctuations are similarly enhanced, even near hydrophobic surfaces of complex biomolecules, situating them at the edge of a dewetting transition.
Journal ArticleDOI
Graphitic carbon-water nonbonded interaction parameters
Yanbin Wu,Narayana R. Aluru +1 more
TL;DR: In this article, the Moller-Plesset perturbation theory of the second order (MP2) was employed to compute the polycyclic aromatic hydrocarbon (PAH)-water interaction energies, with proper size of basis sets and energy component analysis to extrapolate to infinite-sized graphene limit.
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Mechanism of ABC transporters: A molecular dynamics simulation of a well characterized nucleotide-binding subunit
Peter M. Jones,Anthony M. George +1 more
TL;DR: A model for the catalytic cycle of ABC transporters is proposed that shows how substrate-binding and transport by the TMDs may be coordinated and coupled with ATP binding and hydrolysis in the NBDs.
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.