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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] |
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 erro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heat Bath
In thermodynamics, heat is defined as the form of energy crossing the boundary of a thermodynamic system by virtue of a temperature difference across the boundary. A thermodynamic system does not ''contain'' heat. Nevertheless, the term is also often used to refer to the thermal energy contained in a system as a component of its internal energy and that is reflected in the temperature of the system. For both uses of the term, heat is a form of energy. An example of formal vs. informal usage may be obtained from the right-hand photo, in which the metal bar is "conducting heat" from its hot end to its cold end, but if the metal bar is considered a thermodynamic system, then the energy flowing within the metal bar is called internal energy, not heat. The hot metal bar is also transferring heat to its surroundings, a correct statement for both the strict and loose meanings of ''heat''. Another example of informal usage is the term '' heat content'', used despite the fact that ph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kinetic Energy
In physics, the kinetic energy of an object is the energy that it possesses due to its motion. It is defined as the work needed to accelerate a body of a given mass from rest to its stated velocity. Having gained this energy during its acceleration, the body maintains this kinetic energy unless its speed changes. The same amount of work is done by the body when decelerating from its current speed to a state of rest. Formally, a kinetic energy is any term in a system's Lagrangian which includes a derivative with respect to time. In classical mechanics, the kinetic energy of a non-rotating object of mass ''m'' traveling at a speed ''v'' is \fracmv^2. In relativistic mechanics, this is a good approximation only when ''v'' is much less than the speed of light. The standard unit of kinetic energy is the joule, while the English unit of kinetic energy is the foot-pound. History and etymology The adjective ''kinetic'' has its roots in the Greek word κίνησις ''kines ... [...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 e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Flying Ice Cube
In molecular dynamics (MD) simulations, the flying ice cube effect is an artifact in which the energy of high-frequency fundamental modes is drained into low-frequency modes, particularly into zero-frequency motions such as overall translation and rotation of the system. The artifact derives its name from a particularly noticeable manifestation that arises in simulations of particles in vacuum, where the system being simulated acquires high linear momentum and experiences extremely damped internal motions, freezing the system into a single conformation reminiscent of an ice cube or other rigid body flying through space. The artifact is entirely a consequence of molecular dynamics algorithms and is wholly unphysical, since it violates the principle of equipartition of energy. Origin and avoidance The flying ice cube artifact arises from repeated rescalings of the velocities of the particles in the simulation system. Velocity rescaling is a means of imposing a thermostat on the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemistry), force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Software For Molecular Mechanics Modeling
This is a list of computer programs that are predominantly used for molecular mechanics calculations. See also * Car–Parrinello molecular dynamics * Comparison of force-field implementations *Comparison of nucleic acid simulation software * List of molecular graphics systems *List of protein structure prediction software *List of quantum chemistry and solid-state physics software *List of software for Monte Carlo molecular modeling * List of software for nanostructures modeling * Molecular design software *Molecular dynamics *Molecular modeling on GPUs *Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
