|
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and 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, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and 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 the Theoretical and Computational Biophysics group at the Beckman Institute for Advanced Science and Technolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Klaus Schulten
Klaus Schulten (January 12, 1947 – October 31, 2016) was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks. Schulten identified the goal of the life sciences as being to characterize biological systems from the atomic to the cellular level. He used petascale computers, and planned to use exa-scale computers, to model atomic-scale bio-chemical processes. His work made possible the dynamic simulation of the activities of thousands of proteins working together at the macromolecular level. His ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beckman Institute For Advanced Science And Technology
The Beckman Institute for Advanced Science and Technology is a unit of the University of Illinois Urbana-Champaign dedicated to interdisciplinary research. A gift from scientist, businessman, and philanthropist Arnold O. Beckman (1900–2004) and his wife Mabel (1900–1989) led to the building of the Institute which opened in 1989. It is one of five institutions which receive support from the Arnold and Mabel Beckman Foundation on an ongoing basis. Current research at Beckman involves the areas of molecular engineering, intelligent systems, and imaging science. Researchers in these areas work across traditional academic boundaries in scientific projects that can lead to the development of real-world applications in medicine, industry, electronics, and human health across the lifespan. History The Beckman Institute for Advanced Science and Technology has its origins in a 1983 meeting in which chancellor John E. Cribbet, Theodore L. Brown, Mort Weir, Lewis Barron and Ned ... [...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 (Quantum Chemistry Program), ORCA, NWChem, Firefly (computer program), Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly (computer program), 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, 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 (molecular mechanics), Abalone References External links * SourceForgeTwitter {{Chemistry software Computational chemistry software Free sci ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Grace (plotting Tool)
Grace is a free WYSIWYG 2D graph plotting tool, for Unix-like operating systems. The package name stands for "GRaphing, Advanced Computation and Exploration of data." Grace uses the X Window System and Motif for its GUI. It has been ported to VMS, OS/2, and Windows 9*/NT/2000/XP (on Cygwin). In 1996, Linux Journal described Xmgr (an early name for Grace) as one of the two most prominent graphing packages for Linux. History Grace is a descendant of the ACE/gr plotting tool (also known as Xvgr), based on Xview libraries from OpenWindows. Xvgr was originally written by Paul Turner of Portland, Oregon, who continued development until version 4.00. In 1996, development was taken over by the ACE/gr development team, led by Evgeny Stambulchik at the Weizmann Institute of Science, Israel. Development of Xmgr was frozen at version 4.1.2 in 1998 and the Grace project was started as a fork, released under the GPL. The name stands for "GRaphing, Advanced Computation and Exploration ... [...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] |
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 *Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
List Of Molecular Graphics Systems
This is a list of notable software systems that are used for visualizing macromolecules. Key The tables below indicate which types of data can be visualized in each system: See also * Biological data visualization * Comparison of nucleic acid simulation software * Comparison of software for molecular mechanics modeling * List of microscopy visualization systems * List of open-source bioinformatics software * Molecular graphics * Molecule editor A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, v ... References External links * A rather detailed, objective, and technical assessment of about 20 tools. * * * {{Chemistry software Chemistry software molecular graphics systems Molecular modelling ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tk (framework)
Tk is a free and open-source, cross-platform widget toolkit that provides a library of basic elements of GUI widgets for building a graphical user interface (GUI) in many programming languages. Tk provides a number of widgets commonly needed to develop desktop applications, such as button, menu, canvas, text, frame, label, etc. Tk has been ported to run on most flavors of Linux, Mac OS, Unix, and Microsoft Windows. Like Tcl, Tk supports Unicode within the Basic Multilingual Plane, but it has not yet been extended to handle the current extended full Unicode (e.g., UTF-16 from UCS-2 that Tk supports). Tk was designed to be extended, and a wide range of extensions are available that offer new widgets or other capabilities. Since Tcl/Tk 8, it offers "native look and feel" (for instance, menus and buttons are displayed in the manner of "native" software for any given platform). Highlights of version 8.5 include a new theming engine, originally called Tk Tile, but it is now general ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenGL Shading Language
OpenGL Shading Language (GLSL) is a high-level shading language with a syntax based on the C programming language. It was created by the OpenGL ARB (OpenGL Architecture Review Board) to give developers more direct control of the graphics pipeline without having to use ARB assembly language or hardware-specific languages. Background With advances in graphics cards, new features have been added to allow for increased flexibility in the rendering pipeline at the vertex and fragment level. Programmability at this level is achieved with the use of fragment and vertex shaders. Originally, this functionality was achieved by writing shaders in ARB assembly language – a complex and unintuitive task. The OpenGL ARB created the OpenGL Shading Language to provide a more intuitive method for programming the graphics processing unit while maintaining the open standards advantage that has driven OpenGL throughout its history. Originally introduced as an extension to OpenGL 1.4, GLSL was ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Haptic Technology
Haptic technology (also kinaesthetic communication or 3D touch) is technology that can create an experience of touch by applying forces, vibrations, or motions to the user. These technologies can be used to create virtual objects in a computer simulation, to control virtual objects, and to enhance remote control of machines and devices (telerobotics). Haptic devices may incorporate tactile sensors that measure forces exerted by the user on the interface. The word '' haptic'', from the grc-gre, ἁπτικός (''haptikos''), means "tactile, pertaining to the sense of touch". Simple haptic devices are common in the form of game controllers, joysticks, and steering wheels. Haptic technology facilitates investigation of how the human sense of touch works by allowing the creation of controlled haptic virtual objects. Most researchers distinguish three sensory systems related to sense of touch in humans: cutaneous, kinaesthetic and haptic. All perceptions mediated by cutaneous and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenGL
OpenGL (Open Graphics Library) is a cross-language, cross-platform application programming interface (API) for rendering 2D and 3D vector graphics. The API is typically used to interact with a graphics processing unit (GPU), to achieve hardware-accelerated rendering. Silicon Graphics, Inc. (SGI) began developing OpenGL in 1991 and released it on June 30, 1992; applications use it extensively in the fields of computer-aided design (CAD), virtual reality, scientific visualization, information visualization, flight simulation, and video games. Since 2006, OpenGL has been managed by the non-profit technology consortium Khronos Group. Design The OpenGL specification describes an abstract API for drawing 2D and 3D graphics. Although it is possible for the API to be implemented entirely in software, it is designed to be implemented mostly or entirely in hardware. The API is defined as a set of functions which may be called by the client program, alongside a set of named intege ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
