Journal ArticleDOI
Nosé-Hoover chains : the canonical ensemble via continuous dynamics
TLDR
In this paper, a modification of the Nose-Hoover dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose chains, which gives the canonical distribution where the simple formalism fails.Abstract:
Nose has derived a set of dynamical equations that can be shown to give canonically distributed positions and momenta provided the phase space average can be taken into the trajectory average, i.e., the system is ergodic [S. Nose, J. Chem. Phys. 81, 511 (1984), W. G. Hoover, Phys. Rev. A 31, 1695 (1985)]. Unfortunately, the Nose–Hoover dynamics is not ergodic for small or stiff systems. Here a modification of the dynamics is proposed which includes not a single thermostat variable but a chain of variables, Nose–Hoover chains. The ‘‘new’’ dynamics gives the canonical distribution where the simple formalism fails. In addition, the new method is easier to use than an extension [D. Kusnezov, A. Bulgac, and W. Bauer, Ann. Phys. 204, 155 (1990)] which also gives the canonical distribution for stiff cases.read more
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QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials
Paolo Giannozzi,Stefano Baroni,Stefano Baroni,Nicola Bonini,Matteo Calandra,Roberto Car,Carlo Cavazzoni,Davide Ceresoli,Guido L. Chiarotti,Matteo Cococcioni,Ismaila Dabo,Andrea Dal Corso,Andrea Dal Corso,Stefano de Gironcoli,Stefano de Gironcoli,Stefano Fabris,Stefano Fabris,Guido Fratesi,Ralph Gebauer,Ralph Gebauer,Uwe Gerstmann,Christos Gougoussis,Anton Kokalj,Michele Lazzeri,Layla Martin-Samos,Nicola Marzari,Francesco Mauri,Riccardo Mazzarello,Stefano Paolini,Alfredo Pasquarello,Lorenzo Paulatto,Lorenzo Paulatto,Carlo Sbraccia,Sandro Scandolo,Sandro Scandolo,Gabriele Sclauzero,Gabriele Sclauzero,Ari P. Seitsonen,Alexander Smogunov,Paolo Umari,Renata M. Wentzcovitch +40 more
TL;DR: QUANTUM ESPRESSO as discussed by the authors is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave).
Journal ArticleDOI
Canonical sampling through velocity rescaling
TL;DR: In this paper, the authors present a new molecular dynamics algorithm for sampling the canonical distribution, where the velocities of all the particles are rescaled by a properly chosen random factor.
Journal ArticleDOI
Phonons and related crystal properties from density-functional perturbation theory
TL;DR: In this paper, the current status of lattice-dynamical calculations in crystals, using density-functional perturbation theory, with emphasis on the plane-wave pseudopotential method, is reviewed.
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Constant pressure molecular dynamics algorithms
TL;DR: In this paper, a modularly invariant equations of motion are derived that generate the isothermal-isobaric ensemble as their phase space averages, and the resulting methods are tested on two problems, a particle in a one-dimensional periodic potential and a spherical model of C60 in the solid/fluid phase.
Journal ArticleDOI
How Fast-Folding Proteins Fold
TL;DR: Results of atomic-level molecular dynamics simulations of 12 proteins reveal a set of common principles underlying the folding of 12 structurally diverse proteins that spontaneously and repeatedly fold to their experimentally determined native structures.
References
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Journal ArticleDOI
Canonical dynamics: Equilibrium phase-space distributions
TL;DR: The dynamical steady-state probability density is found in an extended phase space with variables x, p/sub x/, V, epsilon-dot, and zeta, where the x are reduced distances and the two variables epsilus-dot andZeta act as thermodynamic friction coefficients.
Journal ArticleDOI
A unified formulation of the constant temperature molecular dynamics methods
TL;DR: In this article, the authors compared the canonical distribution in both momentum and coordinate space with three recently proposed constant temperature molecular dynamics methods by: (i) Nose (Mol. Phys., to be published); (ii) Hoover et al. [Phys. Rev. Lett. 77, 63 (1983); and (iii) Haile and Gupta [J. Chem. Phys. 79, 3067 (1983).
Book
Mathematical Methods of Classical Mechanics
TL;DR: In this paper, Newtonian mechanics: experimental facts investigation of the equations of motion, variational principles Lagrangian mechanics on manifolds oscillations rigid bodies, differential forms symplectic manifolds canonical formalism introduction to pertubation theory.
Journal ArticleDOI
Molecular dynamics simulations at constant pressure and/or temperature
TL;DR: In this paper, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic-isobaric, canonical, and isothermal-isboric ensembles.
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A computer simulation method for the calculation of equilibrium constants for the formation of physical clusters of molecules: Application to small water clusters
TL;DR: In this article, a molecular dynamics computer simulation method for calculating equilibrium constants for the formation of physical clusters of molecules is presented, which is based on Hill's formal theory of physical clustering.