Method molecular dynamics

Both the Monte Carlo and the molecular dynamics methods (see Section III-2B) have been used to obtain theoretical density-versus-depth profiles for a hypothetical liquid-vapor interface. Rice and co-workers (see Refs. 72 and 121) have found that density along the normal to the surface tends to be a... 

Nos e S 1984 A molecular dynamics method for simulations In the canonical ensemble Mol. Phys. 52 255-68... 

Nose S 1984 A unified formulation of the constant-temperature molecular dynamics methods J. Chem. Phys. 81 511-19... 

Parrinello M and Rahman A 1981 Polymorphic transitions In single crystals a new molecular dynamics method J. Appl. Phys. 52 7182-90... 

A comprehensive introduction to the field, covering statistical mechanics, basic Monte Carlo, and molecular dynamics methods, plus some advanced techniques, including computer code. 

Nose, S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52 (1984) 255-268 ibid. A unified formulation of the constant temperature molecular dynamics method. J. Chem. Phys. 81 (1984) 511-519. 

Procacci, P., Darden, T., Marchi, M., A very fast molecular dynamics method to simulate biomolecular systems with realistic electrostatic interactions. J. Phys. Chem. 100 (1996) 10464-10468. 

Martyna, G.J. Adiabatic path integral molecular dynamics methods. I. Theory. J. Chem. Phys. 104 (1996) 2018-2027. 

R. Zhou and B. J. Berne. A new molecular dynamics method combining the reference system propagator algorithm with a fast multipole method for simulating proteins and other complex systems. J. Phys. Chem., 103 9444-9459, 1995. 

Zhou R and B J Berne 1995. A New Molecular Dynamics Method Combining the Reference Sys Propagator Algorithm with a Fast Multipole Method for Simulating Proteins and Ol Complex Systems. Journal of Chemical Physics 103 9444-9459. 

Both molecular dynamics studies and femtosecond laser spectroscopy results show that molecules with a sufficient amount of energy to react often vibrate until the nuclei follow a path that leads to the reaction coordinate. Dynamical calculations, called trajectory calculations, are an application of the molecular dynamics method that can be performed at semiempirical or ah initio levels of theory. See Chapter 19 for further details. 

Explicit solvent methods. Monte Carlo methods are somewhat more popular than molecular dynamics methods. 

The molecular dynamics method is useful for calculating the time-dependent properties of an isolated molecule. However, more often, one is interested in the properties of a molecule that is interacting with other molecules. With HyperChem, you can add solvent molecules to the simulation explicitly, but the addition of many solvent molecules will make the simulation much slower. A faster solution is to simulate the motion of the molecule of interest using Langevin dynamics. 

In principle, we could find the minimum-energy crystal lattice from electronic structure calculations, determine the appropriate A-body interaction potential in the presence of lattice defects, and use molecular dynamics methods to calculate ab initio dynamic macroscale material properties. Some of the problems associated with this approach are considered by Wallace [1]. Because of these problems it is useful to establish a bridge between the micro-... 

I Andricioaei, JE Straub. On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics Methodology, optimization, and application to atomic clusters. J Chem Phys 107 9117-9124, 1997. 

Molecular simulation techniques, namely Monte Carlo and molecular dynamics methods, in which the liquid is regarded as an assembly of interacting particles, are the most popular... 

Molecular dynamics, in contrast to MC simulations, is a typical model in which hydrodynamic effects are incorporated in the behavior of polymer solutions and may be properly accounted for. In the so-called nonequilibrium molecular dynamics method [54], Newton s equations of a (classical) many-particle problem are iteratively solved whereby quantities of both macroscopic and microscopic interest are expressed in terms of the configurational quantities such as the space coordinates or velocities of all particles. In addition, shear flow may be imposed by the homogeneous shear flow algorithm of Evans [56]. 

The simulations to investigate electro-osmosis were carried out using the molecular dynamics method of Murad and Powles [22] described earher. For nonionic polar fluids the solvent molecule was modeled as a rigid homo-nuclear diatomic with charges q and —q on the two active LJ sites. The solute molecules were modeled as spherical LJ particles [26], as were the molecules that constituted the single molecular layer membrane. The effect of uniform external fields with directions either perpendicular to the membrane or along the diagonal direction (i.e. Ex = Ey = E ) was monitored. The simulation system is shown in Fig. 2. The density profiles, mean squared displacement, and movement of the solvent molecules across the membrane were examined, with and without an external held, to establish whether electro-osmosis can take place in polar systems. The results clearly estab-hshed that electro-osmosis can indeed take place in such solutions. 

These apparent restrictions in size and length of simulation time of the fully quantum-mechanical methods or molecular-dynamics methods with continuous degrees of freedom in real space are the basic reason why the direct simulation of lattice models of the Ising type or of solid-on-solid type is still the most popular technique to simulate crystal growth processes. Consequently, a substantial part of this article will deal with scientific problems on those time and length scales which are simultaneously accessible by the experimental STM methods on one hand and by Monte Carlo lattice simulations on the other hand. Even these methods, however, are too microscopic to incorporate the boundary conditions from the laboratory set-up into the models in a reahstic way. Therefore one uses phenomenological models of the phase-field or sharp-interface type, and finally even finite-element methods, to treat the diffusion transport and hydrodynamic convections which control a reahstic crystal growth process from the melt on an industrial scale. 

A full-scale treatment of crystal growth, however, requires methods adapted for larger scales on top of these quantum-mechanical methods, such as effective potential methods like the embedded atom method (EAM) [11] or Stillinger-Weber potentials [10] with three-body forces necessary. The potentials are obtained from quantum mechanical calculations and then used in Monte Carlo or molecular dynamics methods, to be discussed below. 

S. Nose, A molecular dynamics method lor simulations in the canonical ensemble. 

D. J. Tildesley, The Molecular Dynamics Method, Kluwer Academic Publishers, Boston, 1998, 23-47. 

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