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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] |
Bond Stretching Energy
Bond or bonds may refer to: Common meanings * Bond (finance), a type of debt security * Bail bond, a commercial third-party guarantor of surety bonds in the United States * Fidelity bond, a type of insurance policy for employers * Chemical bond, the attraction of atoms, ions or molecules to form chemical compounds * Emotional bond, an emotional attachment between one or more individuals. People * Bond (surname) * Bonds (surname) * Mr. Bond (musician), Austrian rapper Arts and entertainment * James Bond, a series of works about the eponymous fictional character * James Bond (literary character), a British secret agent in a series of novels and films * Bond (string quartet), an Australian/British string quartet ** '' Bond: Video Clip Collection'', a video collection from the band * Bond (Canadian band), a Canadian rock band in the 1970s * ''The Bond'' (2007 book), an American autobiography written by The Three Doctors * '' The Bond'', a 1918 film by Charlie Chaplin supporting ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lennard-Jones Potential
In computational chemistry, molecular physics, and physical chemistry, the Lennard-Jones potential (also termed the LJ potential or 12-6 potential; named for John Lennard-Jones) is an intermolecular pair potential. Out of all the intermolecular potentials, the Lennard-Jones potential is probably the one that has been the most extensively studied. It is considered an archetype model for simple yet realistic intermolecular interactions. The Lennard-Jones potential is often used as a building block in molecular models (a.k.a. force fields) for more complex substances. Many studies of the idealized "Lennard-Jones substance" use the potential to understand the physical nature of matter. Overview The Lennard-Jones potential is a simple model that still manages to describe the essential features of interactions between simple atoms and molecules: Two interacting particles repel each other at very close distance, attract each other at moderate distance, and eventually stop intera ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gradient Descent
Gradient descent is a method for unconstrained mathematical optimization. It is a first-order iterative algorithm for minimizing a differentiable multivariate function. The idea is to take repeated steps in the opposite direction of the gradient (or approximate gradient) of the function at the current point, because this is the direction of steepest descent. Conversely, stepping in the direction of the gradient will lead to a trajectory that maximizes that function; the procedure is then known as ''gradient ascent''. It is particularly useful in machine learning for minimizing the cost or loss function. Gradient descent should not be confused with local search algorithms, although both are iterative methods for optimization. Gradient descent is generally attributed to Augustin-Louis Cauchy, who first suggested it in 1847. Jacques Hadamard independently proposed a similar method in 1907. Its convergence properties for non-linear optimization problems were first studied by Has ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Optimization (mathematics)
Mathematical optimization (alternatively spelled ''optimisation'') or mathematical programming is the selection of a best element, with regard to some criteria, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries. In the more general approach, an optimization problem consists of maxima and minima, maximizing or minimizing a Function of a real variable, real function by systematically choosing Argument of a function, input values from within an allowed set and computing the Value (mathematics), value of the function. The generalization of optimization theory and techniques to other formulations constitutes a large area of applied mathematics. Optimization problems Opti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantum Mechanics
Quantum mechanics is the fundamental physical Scientific theory, theory that describes the behavior of matter and of light; its unusual characteristics typically occur at and below the scale of atoms. Reprinted, Addison-Wesley, 1989, It is the foundation of all quantum physics, which includes quantum chemistry, quantum field theory, quantum technology, and quantum information science. Quantum mechanics can describe many systems that classical physics cannot. Classical physics can describe many aspects of nature at an ordinary (macroscopic and Microscopic scale, (optical) microscopic) scale, but is not sufficient for describing them at very small submicroscopic (atomic and subatomic) scales. Classical mechanics can be derived from quantum mechanics as an approximation that is valid at ordinary scales. Quantum systems have Bound state, bound states that are Quantization (physics), quantized to Discrete mathematics, discrete values of energy, momentum, angular momentum, and ot ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
QM/MM
The hybrid QM/MM (quantum mechanics/molecular mechanics) approach is a molecular simulation method that combines the strengths of ''ab initio'' QM calculations (accuracy) and MM (speed) approaches, thus allowing for the study of chemical processes in solution and in proteins. The QM/MM approach was introduced in the 1976 paper of Warshel and Levitt. They, along with Martin Karplus, won the 2013 Nobel Prize in Chemistry for "the development of multiscale models for complex chemical systems". Efficiency An important advantage of QM/MM methods is their efficiency. The cost of doing classical molecular mechanics (MM) simulations in the most straightforward case scales as ''O''(''N''2), where ''N'' is the number of atoms in the system. This is mainly due to electrostatic interactions term (every particle interacts with everything else). However, use of cutoff radius, periodic pair-list updates and more recently the variations of the particle mesh Ewald (PME) method has reduced th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ergodic Hypothesis
In physics and thermodynamics, the ergodic hypothesis says that, over long periods of time, the time spent by a system in some region of the phase space of microstates with the same energy is proportional to the volume of this region, i.e., that all accessible microstates are equiprobable over a long period of time. Liouville's theorem states that, for a Hamiltonian system, the local density of microstates following a particle path through phase space is constant as viewed by an observer moving with the ensemble (i.e., the convective time derivative is zero). Thus, if the microstates are uniformly distributed in phase space initially, they will remain so at all times. But Liouville's theorem does ''not'' imply that the ergodic hypothesis holds for all Hamiltonian systems. The ergodic hypothesis is often assumed in the statistical analysis of computational physics. The analyst would assume that the average of a process parameter over time and the average over the statistica ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Force Field (chemistry)
In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms (or collections of atoms) within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system on the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference being that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), 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 analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Root-mean-square Error
The root mean square deviation (RMSD) or root mean square error (RMSE) is either one of two closely related and frequently used measures of the differences between true or predicted values on the one hand and observed values or an estimator on the other. The deviation is typically simply a differences of scalars; it can also be generalized to the vector lengths of a displacement, as in the bioinformatics concept of root mean square deviation of atomic positions. RMSD of a sample The RMSD of a sample is the quadratic mean of the differences between the observed values and predicted ones. These deviations are called '' residuals'' when the calculations are performed over the data sample that was used for estimation (and are therefore always in reference to an estimate) and are called ''errors'' (or prediction errors) when computed out-of-sample (aka on the full set, referencing a true value rather than an estimate). The RMSD serves to aggregate the magnitudes of the errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Norman L
Norman or Normans may refer to: Ethnic and cultural identity * The Normans, a people partly descended from Norse Vikings who settled in the territory of Normandy in France in the 9th and 10th centuries ** People or things connected with the Norman conquest of southern Italy in the 11th and 12th centuries ** Normanist theory (also known as Normanism) and anti-Normanism, historical disagreement regarding the origin of Russia, Ukraine, Belarus and their historic predecessor, Kievan Rus' ** Norman dynasty, a series of monarchs in England and Normandy ** Norman architecture, romanesque architecture in England and elsewhere ** Norman language, spoken in Normandy ** People or things connected with the French region of Normandy Arts and entertainment * ''Norman'' (2010 film), a 2010 drama film * ''Norman'' (2016 film), a 2016 drama film * ''Norman'' (TV series), a 1970 British sitcom starring Norman Wisdom * ''The Normans'' (TV series), a documentary * "Norman" (song), a 1962 song w ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fast Multipole Method
__NOTOC__ The fast multipole method (FMM) is a numerical technique that was developed to speed up the calculation of long-ranged forces in the ''n''-body problem. It does this by expanding the system Green's function using a multipole expansion, which allows one to group sources that lie close together and treat them as if they are a single source. The FMM has also been applied in accelerating the iterative solver in the method of moments (MOM) as applied to computational electromagnetics problems, and in particular in computational bioelectromagnetism. The FMM was first introduced in this manner by Leslie Greengard and Vladimir Rokhlin Jr. and is based on the multipole expansion of the vector Helmholtz equation. By treating the interactions between far-away basis functions using the FMM, the corresponding matrix elements do not need to be explicitly stored, resulting in a significant reduction in required memory. If the FMM is then applied in a hierarchical manner, it can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
