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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Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
Richard Štefl,Thomas E. Cheatham,Naděžda Špačková,Eva Fadrná,Imre Berger,Jaroslav Koča,Jiří Šponer +6 more
TL;DR: The simulations suggest that "cross-like" two-stranded assemblies may serve as nucleation centers in the initial formation of parallel stranded G-DNA quadruplexes, proceeding through a series of rearrangements involving trapping of cations, association of additional strands, and progressive slippage of strands toward the full stem.
Journal ArticleDOI
Phase diagram of carbon at high pressures and temperatures.
TL;DR: It is found that above \ensuremath{\sim}6 Mbar the liquid state has approximately sixfold coordination, and, consequently, that the melting temperatures of the solids in this pressure range tend to decrease with increasing pressure.
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Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters
TL;DR: In this article, the authors evaluated the dielectric properties of the simple point charge models SPC and SPC/E, as well as the transferable intermolecular potentials with three point charges TIP3P and its CHARMM modified variant TIP-3Pmod.
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A synthetic antimicrobial peptidomimetic (LTX 109): stereochemical impact on membrane disruption.
Johan Isaksson,Bjørn Olav Brandsdal,Magnus Engqvist,Gøril Eide Flaten,John S. Svendsen,Wenche Stensen +5 more
TL;DR: A strong and unusual dependence on the stereochemistry for a molecule proposed to act on a general membrane mechanism is revealed, found to be reinforced by a significantly improved water solubility of the less active isomers due to a guanidyl-π stacking that helps to solvate the hydrophobic surfaces.
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Unfolding of an α-helix in water
TL;DR: A 1 ns molecular dynamics simulation of an 18‐residue peptide (corresponding to a portion of the H helix of myoglobin) in water provides new information about the detailed mechanisms by which helices are made and broken in aqueous solution.
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.