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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Lipid14: The Amber Lipid Force Field
Callum J. Dickson,Benjamin D. Madej,Åge A. Skjevik,Robin M. Betz,Knut Teigen,Ian R. Gould,Ross C. Walker +6 more
TL;DR: The AMBER lipid force field has been updated to create Lipid14, allowing tensionless simulation of a number of lipid types with the AMBER MD package, and is compatible with theAMBER protein, nucleic acid, carbohydrate, and small molecule force fields.
Journal ArticleDOI
Calculating free energies using average force
Eric Darve,Andrew Pohorille +1 more
TL;DR: In this article, a general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived, defined as the forces acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero.
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Umbrella sampling: Umbrella sampling
TL;DR: In this paper, the authors compare the performance of umbrella sampling, biased molecular dynamics (MD) and other methods, such as thermodynamic integration, slow growth, steered MD, or the Jarzynski-based fast growth technique.
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Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program
Jeffry D. Madura,James M. Briggs,Rebecca C. Wade,Malcolm E. Davis,Brock A. Luty,Andrew Ilin,J. Antosiewicz,Michael K. Gilson,Babak Bagheri,L. Ridgway Scott,J. Andrew McCammon +10 more
TL;DR: A general-purpose Brownian dynamics program that has been developed at the University of Houston is described in this paper, where the diffusion of flexible chains is modeled by the finite difference solutions of the linearized Poisson-Boltzmann equation.
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An Improved GROMOS96 Force Field for Aliphatic Hydrocarbons in the Condensed Phase
TL;DR: The GROMOS96 45A3 parameter set should be suitable for application to lipid aggregates such as membranes and micelles, for mixed systems of aliphatics with or without water, for polymers, and other apolar systems that may interact with different biomolecules.
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.