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Replica Exchange
Parallel tempering in physics and statistics, is a computer simulation method typically used to find the lowest free energy state of a system of many interacting particles at low temperature. That is, the one expected to be observed in reality. It addresses the problem that at high temperature one may have a stable state different from low temperature, whereas simulations at low temperature may become "stuck" in a metastable state. It does this by using the fact that the high temperature simulation may visit states typical of both stable and metastable low temperature states. More specifically, parallel tempering (also known as replica exchange MCMC sampling), is a simulation method aimed at improving the dynamic properties of Monte Carlo method simulations of physical systems, and of Markov chain Monte Carlo (MCMC) sampling methods more generally. The replica exchange method was originally devised by Swendsen and Wang then extended by Geyer and later developed, among othe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Physics
Physics is the natural science that studies matter, its fundamental constituents, its motion and behavior through space and time, and the related entities of energy and force. "Physical science is that department of knowledge which relates to the order of nature, or, in other words, to the regular succession of events." Physics is one of the most fundamental scientific disciplines, with its main goal being to understand how the universe behaves. "Physics is one of the most fundamental of the sciences. Scientists of all disciplines use the ideas of physics, including chemists who study the structure of molecules, paleontologists who try to reconstruct how dinosaurs walked, and climatologists who study how human activities affect the atmosphere and oceans. Physics is also the foundation of all engineering and technology. No engineer could design a flat-screen TV, an interplanetary spacecraft, or even a better mousetrap without first understanding the basic laws of physic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Detailed Balance
The principle of detailed balance can be used in kinetic systems which are decomposed into elementary processes (collisions, or steps, or elementary reactions). It states that at equilibrium, each elementary process is in equilibrium with its reverse process. History The principle of detailed balance was explicitly introduced for collisions by Ludwig Boltzmann. In 1872, he proved his H-theorem using this principle.Boltzmann, L. (1964), Lectures on gas theory, Berkeley, CA, USA: U. of California Press. The arguments in favor of this property are founded upon microscopic reversibility. Tolman, R. C. (1938). ''The Principles of Statistical Mechanics''. Oxford University Press, London, UK. Five years before Boltzmann, James Clerk Maxwell used the principle of detailed balance for gas kinetics with the reference to the principle of sufficient reason. He compared the idea of detailed balance with other types of balancing (like cyclic balance) and found that "Now it is impossible to as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heuristics
A heuristic (; ), or heuristic technique, is any approach to problem solving or self-discovery that employs a practical method that is not guaranteed to be optimal, perfect, or rational, but is nevertheless sufficient for reaching an immediate, short-term goal or approximation. Where finding an optimal solution is impossible or impractical, heuristic methods can be used to speed up the process of finding a satisfactory solution. Heuristics can be mental shortcuts that ease the cognitive load of making a decision. Examples that employ heuristics include using trial and error, a rule of thumb or an ansatz, educated guess. Heuristics are the strategies derived from previous experiences with similar problems. These strategies depend on using readily accessible, though loosely applicable, information to control problem solving in human beings, machines and abstract issues. When an individual applies a heuristic in practice, it generally performs as expected. However it can alternati ... [...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] |
Bennett Acceptance Ratio
The Bennett acceptance ratio method (BAR) is an algorithm for estimating the difference in free energy between two systems (usually the systems will be simulated on the computer). It was suggested by Charles H. Bennett in 1976. Preliminaries Take a system in a certain super (i.e. Gibbs) state. By performing a Metropolis Monte Carlo walk it is possible to sample the landscape of states that the system moves between, using the equation : p(\text_x \rightarrow \text_y) = \min \left(e ^ , 1 \right) = M(\beta \, \Delta U) where Δ''U'' = ''U''(State''y'') − ''U''(State''x'') is the difference in potential energy, β = 1/''kT'' (''T'' is the temperature in kelvins, while ''k'' is the Boltzmann constant), and M(x) \equiv \min(e^ , 1) is the Metropolis function. The resulting states are then sampled according to the Boltzmann distribution of the super state at temperature ''T''. Alternatively, if the system is dynamically simulated in the canonical ensemble (als ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Orac (MD Program)
In computer software, Orac is a classical molecular dynamics program, to simulate complex molecular systems at the atomistic level. In 1989-1990, the code was written originally by Massimo Marchi during his stay at International Business Machines ( IBM), Kingston (USA). In 1995, the code was developed further at the Centre européen de calcul atomique et moléculaire (CECAM). It is written in the programming language Fortran. In 1997, it was released under a GNU General Public License (GPL). The latest release of Orac may be run in parallel using the standard Message Passing Interface (MPI) libraries, allowing replica exchange simulations, multiple walkers metadynamics simulations and multiple steered molecular dynamics nonequilibrium trajectories. See also * Comparison 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 * Comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License. LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms. , it is maintained and distributed by researchers at the Sandia National Laboratories and Temple University. Features For computing efficiency, LAMMPS uses neighbor lists (Verlet lists) to keep track of nearby particles. The lists are optimized for systems with particles that repel at short distances, so that the local density of particles never grows too large. On parallel computers, LAMMPS uses spatial-decomposition techniques to partition the simulatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Desmond (software)
Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional computer clusters. The code uses novel parallel algorithms and numerical methods to achieve high performance on platforms containing multiple processors, but may also be executed on a single computer. The core and source code are available at no cost for non-commercial use by universities and other not-for-profit research institutions, and have been used in the Folding@home distributed computing project. Desmond is available as commercial software through Schrödinger, Inc. Molecular dynamics program Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle mesh Ewald-based methods. Constraints can be enforced using the M-SHAKE algorithm. These methods can be used together with time-scale splitting (RESPA-based) inte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
AMBER
Amber is fossilized tree resin that has been appreciated for its color and natural beauty since Neolithic times. Much valued from antiquity to the present as a gemstone, amber is made into a variety of decorative objects."Amber" (2004). In Maxine N. Lurie and Marc Mappen (eds.) ''Encyclopedia of New Jersey'', Rutgers University Press, . Amber is used in jewelry and has been used as a healing agent in folk medicine. There are five classes of amber, defined on the basis of their chemical constituents. Because it originates as a soft, sticky tree resin, amber sometimes contains animal and plant material as inclusions. Amber occurring in coal seams is also called resinite, and the term ''ambrite'' is applied to that found specifically within New Zealand coal seams. Etymology The English word ''amber'' derives from Arabic (ultimately from Middle Persian ''ambar'') via Middle Latin ''ambar'' and Middle French ''ambre''. The word was adopted in Middle English in the 14th century ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
