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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Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.
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Effect of natural mutations of SARS-CoV-2 on spike structure, conformation and antigenicity
Sophie M. C. Gobeil,Katarzyna Janowska,Shana McDowell,Katayoun Mansouri,Robert Parks,Victoria Stalls,Megan Kopp,Kartik Manne,Kevin O. Saunders,Robert J. Edwards,Barton F. Haynes,Rory Henderson,Priyamvada Acharya +12 more
TL;DR: In this paper, the antigenic and structural impacts of the S protein mutations from four variants, one that was involved in transmission between minks and humans, and three that rapidly spread in human populations and originated in the United Kingdom, Brazil or South Africa.
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Generalized Gaussian moment thermostatting: A new continuous dynamical approach to the canonical ensemble
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TL;DR: Martyna et al. as discussed by the authors proposed a new method for generating the canonical ensemble via continuous dynamics, which is based on controlling the fluctuations of an arbitrary number of moments of the multidimensional Gaussian momentum distribution function.
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Computer simulation studies of the structure I clathrate hydrates of methane, tetrafluoromethane, cyclopropane, and ethylene oxide
TL;DR: In this paper, the results of molecular dynamics simulations on the ice clathrates of methane, tetrafluoromethane, cyclopropane, and ethylene oxide were reported.
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Novel Class of Quinone-Bearing Polyamines as Multi-Target-Directed Ligands To Combat Alzheimer's Disease
Maria Laura Bolognesi,Rita Banzi,Manuela Bartolini,Andrea Cavalli,Andrea Tarozzi,Vincenza Andrisano,Anna Minarini,Michela Rosini,Vincenzo Tumiatti,Christian Bergamini,Romana Fato,Giorgio Lenaz,Patrizia Hrelia,Antonino Cattaneo,Maurizio Recanatini,Carlo Melchiorre +15 more
TL;DR: In this paper, a new class of multi-target-directed ligands (MTDLs) based on a polyamine−quinone skeleton, whose lead (memoquin, 2) showed promising properties in preclinical investigations, is described.
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
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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.