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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Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations
TL;DR: It is shown how the long-time statistical dynamics of a simple solvated biomolecular system can be well described by a discrete-state Markov chain model constructed from trajectories that are an order of magnitude shorter than the longest relaxation times of the system.
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Symplectic Numerical Integrators in Constrained Hamiltonian Systems
TL;DR: In this article, the authors investigated the symplecticness of numerical integrators for constrained dynamics, such as occur in molecular dynamics when bond lengths are made rigid in order to overcome stepsize limitations due to the highest frequencies.
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Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity.
Sophie M. C. Gobeil,Katarzyna Janowska,Shana McDowell,Katayoun Mansouri,Robert Parks,Victoria Stalls,Megan Kopp,Kartik Manne,Dapeng Li,Kevin Wiehe,Kevin Wiehe,Kevin O. Saunders,Robert J. Edwards,Robert J. Edwards,Bette T. Korber,Barton F. Haynes,Barton F. Haynes,Rory Henderson,Rory Henderson,Priyamvada Acharya,Priyamvada Acharya +20 more
TL;DR: In this article, the authors combined cryo-electron microscopy (cryo-EM), binding, and computational analyses to study variant spikes, including one that was involved in transmission between minks and humans, and others that originated and spread in human populations.
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Empirical energy functions for energy minimization and dynamics of nucleic acids
Lennart Nilsson,Martin Karplus +1 more
TL;DR: In this paper, an improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic properties of model systems.
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Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
TL;DR: A unified approach of efficiently sampling both the torsional degrees of freedom and the diffusive motions concurrently is presented and it is shown that this approach samples the configuration space more efficiently than normal molecular dynamics and that ensemble averages converge faster to the correct values.
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.