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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Role of the extracellular loops of G protein-coupled receptors in ligand recognition: a molecular modeling study of the human P2Y1 receptor.
TL;DR: The findings support ATP binding to at least two distinct domains of the P2Y1 receptor, both outside and within the TM core, as well as the selective reduction in potency of 3'NH2-ATP in activating the E209R mutant receptor.
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Dynamics and structure of hydration water on rutile and cassiterite nanopowders studied by quasielastic neutron scattering and molecular dynamics simulations.
Eugene Mamontov,Lukas Vlcek,D. J. Wesolowski,Peter T. Cummings,Wenyong Wang,Lawrence M. Anovitz,Jörgen Rosenqvist,C. M. Brown,⊥,# and,V. García Sakai +8 more
TL;DR: In this paper, the diffusion dynamics of hydration water in nanopowder rutile (TiO2) and cassiterite (SnO2), which possess the same crystal structure with the (110) crystal face predominant on the surface, were analyzed using time-of-flight and backscattering neutron spectrometers.
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Ionic liquids: dissecting the enthalpies of vaporization.
TL;DR: The calculated increase of about 4.7 kJ mol(-1) per CH(2)-group of the van der Waals contribution in the ionic liquid exactly coincides with the increase in the heats of vaporisation for n-alcohols and n-alkanes, respectively.
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Synthesis and Structure−Activity Relationship of a New Series of COX-2 Selective Inhibitors: 1,5-Diarylimidazoles
Carmen Almansa,José Alfón,Alberto Fernández de Arriba,F. L. Cavalcanti,Ignasi Escamilla,L. A. Gomez,Agusti Miralles,Robert Soliva,Javier Bartroli,Elena Carceller,Manuel Merlos,Julian Garcia-Rafanell +11 more
TL;DR: Modification of all the positions of two regioisomeric imidazole cores led to the identification of 4-[4-chloro-5-(3-fluoro-4-methoxyphenyl)imidazol-1-yl]benzenesulfonamide (UR-8880, 51f) as the best candidate, which is now undergoing Phase I clinical trials.
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Structural Equilibrium of DNA Represented with Different Force Fields
Michael Feig,Bernard Pettitt +1 more
TL;DR: A detailed comparison of DNA structure and dynamics for both force fields from extended simulation times of 10 ns each is presented, indicating that convergence times of several nanoseconds are necessary to fully establish a dynamical equilibrium in all structural quantities on the time scale of the simulations presented here.
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.