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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 *Compa ... [...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 err ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Centre Européen De Calcul Atomique Et Moléculaire
Center or centre may refer to: Mathematics *Center (geometry), the middle of an object * Center (algebra), used in various contexts ** Center (group theory) ** Center (ring theory) * Graph center, the set of all vertices of minimum eccentricity Places United States * Centre, Alabama * Center, Colorado * Center, Georgia * Center, Indiana * Center, Jay County, Indiana * Center, Warrick County, Indiana * Center, Kentucky * Center, Missouri * Center, Nebraska * Center, North Dakota * Centre County, Pennsylvania * Center, Portland, Oregon * Center, Texas * Center, Washington * Center, Outagamie County, Wisconsin * Center, Rock County, Wisconsin **Center (community), Wisconsin *Center Township (other) *Centre Township (other) *Centre Avenue (other) *Center Hill (other) Other countries * Centre region, Hainaut, Belgium * Centre Region, Burkina Faso * Centre Region (Cameroon) * Centre-Val de Loire, formerly Centre, France * Centre (department), H ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 *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 This is a list of computer programs that are used to model nanostructures at the levels of classical mechanics and quantum mechanics. Furiousatoms- a powerful software for molecular modelling and visualization * Aionics.io - a powerful platform ... * Molecular design software * Molecular dynamics * Molecular modeling on GPUs * Molecule editor Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Current Opinion In Structural Biology
Currents, Current or The Current may refer to: Science and technology * Current (fluid), the flow of a liquid or a gas ** Air current, a flow of air ** Ocean current, a current in the ocean *** Rip current, a kind of water current ** Current (stream), currents in rivers and streams ** Convection current, flow caused by unstable density variation due to temperature differences * Current (mathematics), geometrical current in differential topology * Conserved current, a field associated to a symmetry in field theory * Electric current, a flow of electric charge through a medium * Probability current, in quantum mechanics * IBM Current, an early personal information management program Arts and entertainment Music * ''Current'' (album), a 1982 album by Heatwave * ''Currents'' (Eisley album) * ''Currents'' (Tame Impala album) * "The Current" (song), by the Blue Man Group * "Currents", a song by Dashboard Confessional from ''Dusk and Summer'', 2006 * "Currents", a song by Drake from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reports On Progress In Physics
''Reports on Progress in Physics'' is a monthly peer-reviewed scientific journal published by IOP Publishing. The editor-in-chief as of 2022 is Subir Sachdev (Harvard University). Scope The focus of this journal is invited review articles covering all branches of 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 r .... Each review will typically survey and critique a particular topic, or developments in a field. Introductions of articles are intended for a broad readership, beyond the specialist or expert. In addition to the traditional review article two other formats are available: ''Reports on Progress'' (about 20 pages) and ''Key Issues Reviews'' (about 10 pages). [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Metadynamics
Metadynamics (MTD; also abbreviated as METAD or MetaD) is a computer simulation method in computational physics, chemistry and biology. It is used to estimate the free energy and other state functions of a system, where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Alessandro Laio and Michele Parrinello in 2002 and is usually applied within molecular dynamics simulations. MTD closely resembles a number of recent methods such as adaptively biased molecular dynamics, adaptive reaction coordinate forces and local elevation umbrella sampling. More recently, both the original and well-tempered metadynamics were derived in the context of importance sampling and shown to be a special case of the adaptive biasing potential setting. MTD is related to the Wang–Landau sampling. Introduction The technique builds on a large number of related methods including (in a chronological order) the deflation, tunneling, tabu search, local elevatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 oth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Computational Chemistry
The ''Journal of Computational Chemistry'' is a peer-reviewed scientific journal published since 1980 by John Wiley & Sons. It covers research, contemporary developments in theory and methodology, and applications in all areas of computational chemistry, including ab initio quantum chemistry methods and semiempirical methods, density functional theory, molecular mechanics, molecular dynamics, statistical mechanics, cheminformatics, biomolecular structure prediction, molecular design, and bioinformatics. According to the ''Journal Citation Reports'', the journal has a 2020 impact factor The impact factor (IF) or journal impact factor (JIF) of an academic journal is a scientometric index calculated by Clarivate that reflects the yearly mean number of citations of articles published in the last two years in a given journal, as ... of 3.376, ranking it 80th out of 179 journals in the category "Chemistry, Multidisciplinary". References External links * {{Official website ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software is a set of computer programs and associated software documentation, documentation and data (computing), data. This is in contrast to Computer hardware, hardware, from which the system is built and which actually performs the work. At the low level language, lowest programming level, executable code consists of Machine code, machine language instructions supported by an individual Microprocessor, processor—typically a central processing unit (CPU) or a graphics processing unit (GPU). Machine language consists of groups of Binary number, binary values signifying Instruction set architecture, processor instructions that change the state of the computer from its preceding state. For example, an instruction may change the value stored in a particular storage location in the computer—an effect that is not directly observable to the user. An instruction System call, may also invoke one of many Input/output, input or output operations, for example displaying some text on ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GNU General Public License
The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end user In product development, an end user (sometimes end-user) is a person who ultimately uses or is intended to ultimately use a product. The end user stands in contrast to users who support or maintain the product, such as sysops, system administrat ...s the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was the first copyleft for general use and was originally written by the founder of the Free Software Foundation (FSF), Richard Stallman, for the GNU Project. The license grants the recipients of a computer program the rights of the Free Software Definition. These GPL series are all copyleft licenses, which means that any derivative work must be distributed under the same or equivalent license terms. It is more restrictive than the GNU Lesser General Public License, Lesser General Public License ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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