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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Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems
TL;DR: A molecular dynamics program for free energy calculations in biomolecular systems is presented in this paper, which is principally designed for free-energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods.
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Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.
TL;DR: Overall this study invites attention to the robustness of the average properties controlled by the low frequency motions, which are invariably reproduced in all approaches, and the utility and efficiency of the ANM, the computational time cost of which is of the order of “minutes” (real time) as opposed to “days” for MD simulations.
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Computational alanine scanning of the 1:1 human growth hormone–receptor complex
TL;DR: It is demonstrated that a separate trajectory of the alanine mutant complex can lead to reasonable agreement with experimental results and the MM‐PBSA approach can be extended to rapid screening of a variety of possible modifications to binding sites.
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Molecular dynamics simulation of a phospholipid membrane
TL;DR: Comparison of MD results with reliable experimental data showed that the simulations, especially the one in the liquid-crystalline phase, can serve as a realistic model for a phospholipid membrane, including full atomic detail.
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On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.
TL;DR: Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, it is obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces.
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.