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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Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field
TL;DR: Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydrations free energies.
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Application of molecular dynamics simulations in molecular property prediction II: Diffusion coefficient
Junmei Wang,Tingjun Hou +1 more
TL;DR: It is concluded that the sampling strategy that averaging the mean square displacement collected in multiple short‐MD simulations is efficient in predicting diffusion coefficients of solutes at infinite dilution.
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Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model
Asim Okur,Lauren Wickstrom,Melinda Layten,Raphaël Geney,Kun Song,and Viktor Hornak,Carlos Simmerling +6 more
TL;DR: An REMD variant in which the simulations are performed with a fully explicit solvent, but the calculation of exchange probability is carried out using a hybrid model, with the solvation shells calculated on the fly during the fully solvated simulation providing a dramatic decrease in the computational cost of REMD.
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Combined Static and Dynamic Density Functional Study of the Ti(IV) Constrained Geometry Catalyst (CpSiH2NH)TiR+. 1. Resting States and Chain Propagation
TL;DR: In this paper, the first molecular dynamics simulation specifically addressing the structure of a metallocene−alkyl cation is presented showing rapid interconversion between γ- and β-agostic conformations.
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Simulation Studies of Stratum Corneum Lipid Mixtures
TL;DR: Close to the skin composition ratio, the lateral pressure fluctuations are greatly suppressed, the ceramide tails from the two leaflets interdigitate significantly, the depression in local density at the interleaflet region is lowered, and the bilayers have lowered elastic moduli, indicating that the observed composition ratio in the stratum corneum lipid layer is responsible for both the good barrier properties and the stability of the lipid structure against mechanical stresses.
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.