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Extensible Computational Chemistry Environment
The Extensible Computational Chemistry Environment (ECCE, pronounced "etch-ā") provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. Major features * Support for building molecular models. * Graphical user interface to a broad range of electronic structure theory types. Supported codes currently include NWChem, GAMESS (UK), Gaussian 03, Gaussian 98, and Amica. Other codes are registered based on user requirements. * Graphical user interface for basis set selection. * Remote submission of calculations to UNIX and Linux workstations, Linux clusters, and supercomputers. Supported queue management systems include PBS, LSF, NQE/NQS, LoadLeveler and Maui Scheduler. * Three-dimensional visualization and graphical display of molecular data pro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pacific Northwest National Laboratory
Pacific Northwest National Laboratory (PNNL) is one of the United States Department of Energy national laboratories, managed by the Department of Energy's (DOE) Office of Science. The main campus of the laboratory is in Richland, Washington, with additional research facilities around the country. Originally named the Pacific Northwest Laboratory, PNL was established in 1965 when research and development at the Hanford Site was separated from other Hanford operations. In 1995, the laboratory was renamed the Pacific Northwest National Laboratory (PNNL). Research facilities The Environmental Molecular Sciences Laboratory (EMSL) is a U.S. Department of Energy national scientific user facility. EMSL provides researchers around the world with integrated capabilities in oxide and mineral interface chemistry, high-performance computing and computational chemistry software, mass spectrometry, high-field magnetic resonance, and subsurface flow and transport research. The Biopr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cluster (computing)
A computer cluster is a set of computers that work together so that they can be viewed as a single system. Unlike Grid computing, grid computers, computer clusters have each Node (networking), node set to perform the same task, controlled and scheduled by software. The newest manifestation of cluster computing is cloud computing. The components of a cluster are usually connected to each other through fast local area networks, with each Node (networking), node (computer used as a server) running its own instance of an operating system. In most circumstances, all of the nodes use the same hardware and the same operating system, although in some setups (e.g. using Open Source Cluster Application Resources (OSCAR)), different operating systems can be used on each computer, or different hardware. Clusters are usually deployed to improve performance and availability over that of a single computer, while typically being much more cost-effective than single computers of comparable s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ascalaph Designer
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly (formerly named PC GAMESS) covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2). Key features Uses See also * List of software for molecular mechanics modeling * Molecular design software * Molecule editor * Abalone Abalone ( or ; via Spanish , from Rumsen language, Rumsen ''aulón'') is a common name for any small to very large marine life, marine gastropod mollusc in the family (biology), family Haliotidae, which once contained six genera but now cont ... References Exter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RasMol
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank (PDB). History It was originally developed by Roger Sayle in the early 1990s. Historically, it was an important tool for molecular biologists since the extremely optimized program allowed the software to run on (then) modestly powerful personal computers. Before RasMol, visualization software ran on graphics workstations that, due to their cost, were less accessible to scholars. RasMol continues to be important for research in structural biology, and has become important in education. RasMol has a complex licensing version history. Starting with the version 2.7 series, RasMol source code is dual-licensed under a GNU General Public License (GPL), or custom license ''RASLIC''. Starting with version 2.7.5, a GPL is the only license valid for binary distributions. RasMol include ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jmol
Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. It can hence be embedded in web pages to display interactive 3D models of molecules and other structures without the need for any software apart from the web browser (''it does not use Java''). Both Jmol and JSmol render an interactive 3D representation of a molecule or other structure that may be used as a teaching tool, or for research, in several fields, e.g. chemistry, biochemistry, materials science, crystallography, symmetry or nanotechnology. Software Jmol is written in the programming language Java, so it can run on different operating systems: Windows, macOS, Linux, and Unix, as long as they have Java installed. It is free and open-source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan (software), RenderMan, Tachyon (software), Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python (programming language), Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. History VMD has been developed under the aegis of principal investigator Klaus Schulten in th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PyMol
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrödinger, LLC.), and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The ''Py'' part of the software's name refe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molekel
Molekel is a free software multiplatform molecular visualization program. It was originally developed at the University of Geneva by Peter F. Flükiger in the 1990s for Silicon Graphics Computers. In 1998, Stefan Portmann took over responsibility and released Version 3.0. Version 4.0 was a nearly platform independent version. Further developments lead to version 4.3, before Stefan Portmann moved on and ceased to develop the codes. In 2006, the Swiss National Supercomputing Centre (CSCS) restarted the project and version 5.0 was released on 21 December 2006. Molekel uses VTK and Qwt and therefore as well Qt. Major features * Visu ...[...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gabedit
Gabedit is a graphical user interface to GAMESS (US), Gaussian, MOLCAS, MOLPRO, MPQC, OpenMopac, PC GAMESS, ORCA and Q-Chem computational chemistry packages. Major features * Builds molecules by atom, ring, group, amino acid and nucleoside. * Creates an input file for computational chemistry packages. * Reads output from the ab initio packages, and supports a number of other formats. * Displays molecular orbitals or electron density as contour plots or 3D grid plots and output to a number of graphical formats. * Animates molecular vibrations, contours, isosurfaces and rotation. See also * List of molecular graphics systems * PC GAMESS * ORCA * Quantum chemistry computer programs Quantum chemistry computer programs are used in computational chemistry to implement the methods of quantum chemistry. Most include the Hartree–Fock (HF) and some post-Hartree–Fock methods. They may also include density functional theory (DFT) ... * SAMSON External links Gabedit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Avogadro (software)
Avogadro is a molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It is extensible via a plugin architecture. Features * Molecule builder-editor for Microsoft Windows, Windows, Linux, Unix, and macOS. * All source code is licensed under the GNU General Public License (GPL) version 2. * Supported languages include: Chinese language, Chinese, English language, English, French language, French, German language, German, Italian language, Italian, Russian language, Russian, Spanish language, Spanish, and Polish language, Polish. * Supports thread (computer science), multi-threaded Rendering (computer graphics), rendering and computation. * Plugin architecture for developers, including rendering, interactive tools, commands, and Python (programming language), Python scripts. * OpenBabel import of files, input generation for multiple computational chemistry packages, X-ray c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molden
Molden is a general molecular and electronic structure processing program. Major features * Reads output from the ab initio packages GAMESS (US), Gaussian, MOLPRO, PySCF and from semi-empirical packages such as MOPAC, and supports a number of other formats. * Displays molecular orbitals or electron density Electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typical ... as contour plots or 3D grid plots and output to a number of graphical formats. * Animates reaction paths and molecular vibrations. * A Z-matrix editor. Molden program has been tested on different platforms, namely Linux, Windows NT, Windows95, Windows2000, WindowsXP, MacOSX, Silicon Graphics IRIX, Sun SunOS and Solaris. Ambfor, the main force field module of Molden, is an external program that can be initialized from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
