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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The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant
TL;DR: A systematic study of the entropy term in the MM/GBSA (molecular mechanics combined with generalized Born and surface-area solvation) approach to calculate ligand-binding affinities shows that removing protein residues with distances larger than 8-16 Å to the ligand changes the absolute entropies by 1-5 kJ/mol on average.
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Pulling direction as a reaction coordinate for the mechanical unfolding of single molecules.
TL;DR: This work applies a recent theoretical approach describing molecular rupture in the presence of force to unfolding kinetic data obtained from coarse-grained simulations of ubiquitin, and relates the turnover to the quality of the pulling direction as a reaction coordinate for the intrinsic folding mechanism.
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Hydrogen bonding in 1-butyl- and 1-ethyl-3-methylimidazolium chloride ionic liquids.
TL;DR: Analyses of the individual atom-atom pair radial distribution functions, and in particular those for C···Cl(-), have revealed that hydrogen bonding to the first methylene or methyl units of the substituent groups is important.
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Distinct aggregation mechanisms of monoclonal antibody under thermal and freeze-thaw stresses revealed by hydrogen exchange.
TL;DR: Reduced hydrogen exchange in three CDRs suggests these residues may form strong intermolecular contacts in the antibody aggregates; regions of enhanced HX indicate unfolding.
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Molecular picture of folding of a small α/β protein
TL;DR: The mechanism and thermodynamics of small α/β protein folding were characterized at the atomic level in this paper by using the statistical mechanical methods of importance sampling and molecular dynamics, showing that the α-helix forms early and the β-sheet forms concomitantly with the overall topology.
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.