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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Structure of a Signaling Cannabinoid Receptor 1-G Protein Complex
Kaavya Krishna Kumar,Moran Shalev-Benami,Michael J. Robertson,Hongli Hu,Samuel D. Banister,Scott A. Hollingsworth,Naomi R. Latorraca,Hideaki E. Kato,Daniel Hilger,Shoji Maeda,William I. Weis,William I. Weis,David L. Farrens,Ron O. Dror,Sanjay V. Malhotra,Brian K. Kobilka,Georgios Skiniotis,Georgios Skiniotis +17 more
TL;DR: The structure of the CB1-Gi signaling complex bound to the highly potent agonist MDMB-Fubinaca (FUB) is presented, which compose the structural framework to explain CB1 activation by different classes of ligands and provide insights into the G protein coupling and selectivity mechanisms adopted by the receptor.
Journal ArticleDOI
Systematic Parameterization of Monovalent Ions Employing the Nonbonded Model.
TL;DR: The 12-6 LJ parameters for 15 monovalent ions are reoptimized for three extensively used water models using a noble gas curve and the final parameter sets showed better agreement with quantum mechanically calculated VDW radii and improved transferability to ion-pair solutions when compared to previous parameter sets.
Journal ArticleDOI
Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations.
TL;DR: All the nonlinear methods yield similar results if extensive sampling is performed, but soft core scaling provides smooth lambda curves that are best suited for commonly used numerical integration schemes.
Journal ArticleDOI
Blue Gene: a vision for protein science using a petaflop supercomputer
F. E. Allen,George Almási,Wanda Andreoni,D. Beece,Bruce J. Berne,A. A. Bright,Jose R. Brunheroto,Calin Cascaval,José G. Castaños,Paul W. Coteus,Paul G. Crumley,Alessandro Curioni,Monty M. Denneau,Wilm E. Donath,Maria Eleftheriou,Blake G. Fitch,Bruce M. Fleischer,Christos John Georgiou,Robert S. Germain,Mark E. Giampapa,Donna L. Gresh,Manish Gupta,R. A. Haring,H. Ho,Peter H. Hochschild,Susan Flynn Hummel,T. Jonas,Derek Lieber,Glenn J. Martyna,K. Maturu,José E. Moreira,D.M. Newns,M. Newton,Robert Alan Philhower,T. Picunko,Jed W. Pitera,Michael C. Pitman,Rick A. Rand,Ajay K. Royyuru,Valentina Salapura,A. Sanomiya,R. Shah,Yuk Y. Sham,Suryabhan Singh,Marc Snir,Frank Suits,Richard A. Swetz,William C. Swope,N. Vishnumurthy,T.J.C. Ward,Henry S. Warren,Ruhong Zhou +51 more
TL;DR: An overview of the Blue Gene project at IBM Research is provided to advance the understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively parallel machine architecture and software.
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A new GROMOS force field for hexopyranose-based carbohydrates
TL;DR: A new parameter set (referred to as 45A4) is developed for the explicit‐solvent simulation of hexopyranose‐based carbohydrates and is validated for a limited set of monosaccharide and disaccharides in solution, by comparing the results of simulations to available experimental data.
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.