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Nosé–Hoover Thermostat
The Nosé–Hoover thermostat is a deterministic algorithm for constant-temperature molecular dynamics simulations. It was originally developed by Nosé and was improved further by Hoover. Although the heat bath of Nosé–Hoover thermostat consists of only one imaginary particle, simulation systems achieve realistic constant-temperature condition (canonical ensemble). Therefore, the Nosé–Hoover thermostat has been commonly used as one of the most accurate and efficient methods for constant-temperature molecular dynamics simulations. Introduction In classical molecular dynamics, simulations are done in the microcanonical ensemble; a number of particles, volume, and energy have a constant value. In experiments, however, the temperature is generally controlled instead of the energy. The ensemble of this experimental condition is called a canonical ensemble. Importantly, the canonical ensemble is different from microcanonical ensemble from the viewpoint of statistical mechanics. Se ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Shuichi Nosé
was a Japanese physicist. Nosé is best known for his two 1984 papers in which he proposed a method to specify the temperature of molecular dynamics simulations. This method was later improved by William G. Hoover and is known as the Nosé–Hoover thermostat The Nosé–Hoover thermostat is a deterministic algorithm for constant-temperature molecular dynamics simulations. It was originally developed by Nosé and was improved further by Hoover. Although the heat bath of Nosé–Hoover thermostat consis .... Publications * * References Obituaries: * * "Nosé Shuichi, In Memoriam" by William Graham Hoover External links (Japanese) - Awarded for Nose's thermostat. * - Some of notes of Nosé before his death are available. 1951 births 2005 deaths Japanese physicists Academic staff of Keio University Kyoto University alumni {{physicist-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
William G
William is a male given name of Germanic origin.Hanks, Hardcastle and Hodges, ''Oxford Dictionary of First Names'', Oxford University Press, 2nd edition, , p. 276. It became very popular in the English language after the Norman conquest of England in 1066,All Things William"Meaning & Origin of the Name"/ref> and remained so throughout the Middle Ages and into the modern era. It is sometimes abbreviated "Wm." Shortened familiar versions in English include Will, Wills, Willy, Willie, Bill, and Billy. A common Irish form is Liam. Scottish diminutives include Wull, Willie or Wullie (as in Oor Wullie or the play ''Douglas''). Female forms are Willa, Willemina, Wilma and Wilhelmina. Etymology William is related to the given name ''Wilhelm'' (cf. Proto-Germanic ᚹᛁᛚᛃᚨᚺᛖᛚᛗᚨᛉ, ''*Wiljahelmaz'' > German ''Wilhelm'' and Old Norse ᚢᛁᛚᛋᛅᚼᛅᛚᛘᛅᛋ, ''Vilhjálmr''). By regular sound changes, the native, inherited English form of the name shoul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Canonical Ensemble
In statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat bath, so that the states of the system will differ in total energy. The principal thermodynamic variable of the canonical ensemble, determining the probability distribution of states, is the absolute temperature (symbol: ). The ensemble typically also depends on mechanical variables such as the number of particles in the system (symbol: ) and the system's volume (symbol: ), each of which influence the nature of the system's internal states. An ensemble with these three parameters is sometimes called the ensemble. The canonical ensemble assigns a probability to each distinct microstate given by the following exponential: :P = e^, where is the total energy of the microstate, and is the Boltzmann constant. The number is the free ener ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Microcanonical Ensemble
In statistical mechanics, the microcanonical ensemble is a statistical ensemble that represents the possible states of a mechanical system whose total energy is exactly specified. The system is assumed to be isolated in the sense that it cannot exchange energy or particles with its environment, so that (by conservation of energy) the energy of the system does not change with time. The primary macroscopic variables of the microcanonical ensemble are the total number of particles in the system (symbol: ), the system's volume (symbol: ), as well as the total energy in the system (symbol: ). Each of these is assumed to be constant in the ensemble. For this reason, the microcanonical ensemble is sometimes called the ensemble. In simple terms, the microcanonical ensemble is defined by assigning an equal probability to every microstate whose energy falls within a range centered at . All other microstates are given a probability of zero. Since the probabilities must add up to 1, the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Berendsen Thermostat
The Berendsen thermostat is an algorithm to re-scale the velocities of particles in molecular dynamics simulations to control the simulation temperature. Basic description In this scheme, the system is weakly coupled to a heat bath with some temperature. The thermostat suppresses fluctuations of the kinetic energy of the system and therefore cannot produce trajectories consistent with the canonical ensemble. The temperature of the system is corrected such that the deviation exponentially decays with some time constant \tau . :\frac=\frac Though the thermostat does not generate a correct canonical ensemble (especially for small systems), for large systems on the order of hundreds or thousands of atoms/molecules, the approximation yields roughly correct results for most calculated properties. The scheme is widely used due to the efficiency with which it relaxes a system to some target (bath) temperature. In many instances, systems are initially equilibrated using the Berendsen scheme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Langevin Dynamics
In physics, Langevin dynamics is an approach to the mathematical modeling of the dynamics of molecular systems. It was originally developed by French physicist Paul Langevin. The approach is characterized by the use of simplified models while accounting for omitted degrees of freedom by the use of stochastic differential equations. Langevin dynamics simulations are a kind of Monte Carlo simulation. Overview A real world molecular system is unlikely to be present in vacuum. Jostling of solvent or air molecules causes friction, and the occasional high velocity collision will perturb the system. Langevin dynamics attempts to extend molecular dynamics to allow for these effects. Also, Langevin dynamics allows temperature to be controlled like with a thermostat, thus approximating the canonical ensemble. Langevin dynamics mimics the viscous aspect of a solvent. It does not fully model an implicit solvent; specifically, the model does not account for the electrostatic screening and al ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
