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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RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin.
Pascal Auffinger,Eric Westhof +1 more
TL;DR: Simulation results confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure and suggest that RNA and water together constitute the biologically relevant functional entity.
Journal ArticleDOI
Global Fold Determination from a Small Number of Distance Restraints
TL;DR: The method successfully identified the correct folds of three small proteins from a small number of restraints, indicating that it could serve as a useful computational tool in protein structure determination from NMR data.
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QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.
Hao Hu,Zhenyu Lu,Weitao Yang +2 more
TL;DR: The combination of the methods developed here presents a comprehensive and accurate treatment for the simulation of reaction processes in solution and in enzymes with ab initio QM/MM methods.
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The reaction mechanism of paraoxon hydrolysis by phosphotriesterase from combined QM/MM simulations.
Kin Yiu Wong,Jiali Gao +1 more
TL;DR: A dual-level QM/MM approach is used that synthesizes accurate results from high-level electronic structure calculations with computational efficiency of semiempirical QM /MM potentials for free energy simulations to suggest a revised mechanism for the phosphotriester hydrolysis mechanism by PTE.
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Molecular Dynamics Simulations in the Grand Canonical Ensemble: Application to Clay Mineral Swelling
Robert M. Shroll,David Smith +1 more
TL;DR: In this paper, a GMD simulation method was adapted to examine the thermodynamics of clay-mineral hydration, where the number of water molecules in the system is treated as a continuous variable for which an equation of motion is established.
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.