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Journal ArticleDOI

Canonical dynamics: Equilibrium phase-space distributions

William G. Hoover
- 01 Mar 1985 - 
- Vol. 31, Iss: 3, pp 1695-1697
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TLDR
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.
Abstract
Nos\'e has modified Newtonian dynamics so as to reproduce both the canonical and the isothermal-isobaric probability densities in the phase space of an N-body system. He did this by scaling time (with s) and distance (with ${V}^{1/D}$ in D dimensions) through Lagrangian equations of motion. The dynamical equations describe the evolution of these two scaling variables and their two conjugate momenta ${p}_{s}$ and ${p}_{v}$. Here we develop a slightly different set of equations, free of time scaling. We find the dynamical steady-state probability density in an extended phase space with variables x, ${p}_{x}$, V, \ensuremath{\epsilon}\ifmmode \dot{}\else \.{}\fi{}, and \ensuremath{\zeta}, where the x are reduced distances and the two variables \ensuremath{\epsilon}\ifmmode \dot{}\else \.{}\fi{} and \ensuremath{\zeta} act as thermodynamic friction coefficients. We find that these friction coefficients have Gaussian distributions. From the distributions the extent of small-system non-Newtonian behavior can be estimated. We illustrate the dynamical equations by considering their application to the simplest possible case, a one-dimensional classical harmonic oscillator.

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TL;DR: This article presents a simple approach to introduce metal polarization effects (often termed image effects) in MD simulations by exploiting standard features of bio‐oriented MD codes such as the widely used GROMACS and NAMD.
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TL;DR: Water dipole moments are observed to exhibit little change during dissociation, indicating that description of NaCl with a nonpolarizable force field may be feasible, however, overcoordination of the ion pair at all distances remains as a serious shortcoming of the current classical models.
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A general-purpose coarse-grained molecular dynamics program

TL;DR: The coarse-grained molecular dynamics program COGNAC (COarse Grained Molecular Dynamics Program by NAgoya Cooperation) as discussed by the authors has been developed for general molecular dynamics simulation, especially for coarsegrained polymer chain models.
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