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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] |
Sandia National Laboratories
Sandia National Laboratories (SNL), also known as Sandia, is one of three research and development laboratories of the United States Department of Energy's National Nuclear Security Administration (NNSA). Headquartered in Kirtland Air Force Base in Albuquerque, New Mexico, it has a second principal facility next to Lawrence Livermore National Laboratory in California and a test facility in Waimea, Kauai, Hawaii. Sandia is owned by the U.S. federal government but privately managed and operated by National Technology and Engineering Solutions of Sandia, a wholly owned subsidiary of Honeywell International. Established in 1949, SNL is a "multimission laboratory" with the primary goal of advancing U.S. national security by developing various science-based technologies. Its work spans roughly 70 areas of activity, including nuclear deterrence, arms control, nonproliferation, hazardous waste disposal, and climate change. Sandia hosts a wide variety of research initiatives, includ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Free And Open-source Software Packages
This is a list of free and open-source software packages, computer software licensed under free software licenses and open-source licenses. Software that fits the Free Software Definition may be more appropriately called free software; the GNU project in particular objects to their works being referred to as open-source. For more information about the philosophical background for open-source software, see free software movement and Open Source Initiative. However, nearly all software meeting the Free Software Definition also meets ''the Open Source Definition'' and vice versa. A small fraction of the software that meets either definition is listed here. Some of the open-source applications are also the basis of commercial products, shown in the List of commercial open-source applications and services. Artificial intelligence General AI *OpenCog – A project that aims to build an artificial general intelligence (AGI) framework. OpenCog Prime is a specific set of interacting ... [...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 * Molecular design software *Molecular dynamics *Molecular modeling on GPUs Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. In 2007, NVIDIA introduced video cards that could be used not only to show graphics but also for scientific calculations. These cards ... * Molecule editor Notes and references External linksSINCRIS [...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] |
Molecular Dynamics Software
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are typically not considere ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Design Software
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models ''de novo''. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software ''directly'' supports the aspects related to constructing molecular models, including: * Molecular graphics * interactive molecular drawing and conformational editing * building polymeric molecules, crystals, and solvated systems * partial charges development * geometry optimization * support for the different aspects of force field development Comparison of software covering the major aspects of molecular design Notes and references See also {{columns-list, colwidth=30em, *Molecule editor *Molecular modelling *Molecular modeling on GPUs *Protein design *Drug design *Force field (chemistry) *Comparison of force field implementations *Comparison of nucleic acid simulation software *Comparison of software fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Parallel Computing
Parallel computing is a type of computation in which many calculations or processes are carried out simultaneously. Large problems can often be divided into smaller ones, which can then be solved at the same time. There are several different forms of parallel computing: bit-level, instruction-level, data, and task parallelism. Parallelism has long been employed in high-performance computing, but has gained broader interest due to the physical constraints preventing frequency scaling.S.V. Adve ''et al.'' (November 2008)"Parallel Computing Research at Illinois: The UPCRC Agenda" (PDF). Parallel@Illinois, University of Illinois at Urbana-Champaign. "The main techniques for these performance benefits—increased clock frequency and smarter but increasingly complex architectures—are now hitting the so-called power wall. The computer industry has accepted that future performance increases must largely come from increasing the number of processors (or cores) on a die, rather tha ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Verlet List
A Verlet list (named after Loup Verlet) is a data structure in molecular dynamics simulations to efficiently maintain a list of all particles within a given cut-off distance of each other. This method may easily be applied to Monte Carlo simulations. For short-range interactions, a cut-off radius is typically used, beyond which particle interactions are considered "close enough" to zero to be safely ignored. For each particle, a Verlet list is constructed that lists all other particles within the potential cut-off distance, plus some extra distance so that the list may be used for several consecutive Monte Carlo "sweeps" (set of Monte Carlo steps or moves) before being updated. If we wish to use the same Verlet list n times before updating, then the cut-off distance for inclusion in the Verlet list should be R_c + 2nd, where R_c is the cut-off distance of the potential, and d is the maximum Monte Carlo step (move) of a single particle. Thus, we will spend of order N^2 time to compute ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
United States Department Of Energy
The United States Department of Energy (DOE) is an executive department of the U.S. federal government that oversees U.S. national energy policy and manages the research and development of nuclear power and nuclear weapons in the United States. The DOE oversees the U.S. nuclear weapons program, nuclear reactor production for the United States Navy, energy-related research, and domestic energy production and energy conservation. The DOE was created in 1977 in the aftermath of the 1973 oil crisis. It sponsors more physical science research than any other U.S. federal agency, the majority of which is conducted through its system of National Laboratories. The DOE also directs research in genomics, with the Human Genome Project originating from a DOE initiative. The department is headed by the Secretary of Energy, who reports directly to the president of the United States and is a member of the Cabinet. The current Secretary of Energy is Jennifer Granholm, who has served ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cooperative Research And Development Agreement
In the United States, a cooperative research and development agreement (CRADA or CRDA) is an agreement between a government agency and another government agency, a private company, non-profit, or university to work together on research and development. Description Designated under the Federal Technology Transfer Act of 1986 (P.L. 99-502) (which amended the Stevenson-Wydler Technology Innovation Act of 1980 (P.L. 96-480)), a CRADA is intended to speed the commercialization of technology, optimize resources, and protect the private company involved. A CRADA allows both parties to keep research results confidential for up to five years under the Freedom of Information Act. The Office of Scientific and Technical Information (OSTI) is responsible for preserving the scientific and technical information generated through a CRADA and making this information readily available to the scientific community as well as the public. Private corporations participating in a CRADA are allowed to f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free And Open-source Software
Free and open-source software (FOSS) is a term used to refer to groups of software consisting of both free software and open-source software where anyone is freely licensed to use, copy, study, and change the software in any way, and the source code is openly shared so that people are encouraged to voluntarily improve the design of the software. This is in contrast to proprietary software, where the software is under restrictive copyright licensing and the source code is usually hidden from the users. FOSS maintains the software user's civil liberty rights (see the Four Essential Freedoms, below). Other benefits of using FOSS can include decreased software costs, increased security and stability (especially in regard to malware), protecting privacy, education, and giving users more control over their own hardware. Free and open-source operating systems such as Linux and descendants of BSD are widely utilized today, powering millions of servers, desktops, smartphones (e.g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
