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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] [Amazon] |
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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 res ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 Goldwas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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] [Amazon] |
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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] [Amazon] |
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Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), 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 analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 *PyMOL Notes and references External linksSINCRIS [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 notable 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 ... References External links * A rather detailed, objective, and technical assessment of about 20 tools. * * * {{Chemistry software Chemistry software molecular graphics systems Molecular modelling Computational chemistry software ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulations 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. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion (dihydrogen cation), achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena. Overview Computational chemistry differs from theoretical chemistry, which involves a mathematical description of chem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Tk (framework)
Tk is a 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. It is free and open-source software released under a BSD-style software license. Tk provides many 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, macOS, 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |