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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Algorithmic Challenges in Computational Molecular Biophysics
Tamar Schlick,Robert D. Skeel,Axel T. Brunger,Laxmikant V. Kale,John A. Board,Jan Hermans,Klaus Schulten +6 more
TL;DR: A perspective of biomolecular simulations today is given, with illustrative applications and an emphasis on algorithmic challenges, as reflected by the work of a multidisciplinary team of investigators from five institutions.
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Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
Huiyong Sun,Lili Duan,Fu Chen,Hui Liu,Zhe Wang,Peichen Pan,Feng Zhu,John Z. H. Zhang,John Z. H. Zhang,Tingjun Hou +9 more
TL;DR: The results show that the ff03 force field performs the best, but the predictions given by the tested force fields are comparable, implying that the MM/GBSA predictions are not very sensitive to force fields.
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Revisiting the finite temperature string method for the calculation of reaction tubes and free energies.
TL;DR: An improved and simplified version of the finite temperature string (FTS) method that calculates the principal curves associated with the Boltzmann-Gibbs probability distribution of the system via sampling in the Voronoi tessellation whose generating points are the discretization points along this curve.
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Dynamics of Asp23-Lys28 salt-bridge formation in Aβ10- 35 monomers
TL;DR: The results suggest that the early event in the oligomerization process must be the expulsion of discrete water molecules that facilitates the formation of interpeptide-interaction-driven stable structures with an intramolecular D23-K28 salt bridge and an intact VGSN turn.
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Mapping hydrophobicity at the nanoscale: Applications to heterogeneous surfaces and proteins
TL;DR: This work uses extensive molecular simulations to study the hydration of homo and heterogeneous self-assembled monolayers (SAMs) and of protein surfaces and presents a more refined picture of its hydrophobicity map.
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.