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MDynaMix
Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like Force field (chemistry), force fields in periodic boundary conditions. Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90 (with Message Passing Interface (MPI) for parallel execution). The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Microsoft Windows, Windows in sequential mode. MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL). Programs * ''md'' is the main MDynaMix block * ''makemol'' is a utility which provides help to create files describing molecular stru ... [...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] |
MacroModel
MacroModel is a computer program for molecular modelling of organic compounds and biopolymers. It features various chemistry force fields, plus energy minimizing algorithms, to predict geometry and relative conformational energies of molecules. MacroModel is maintained by Schrödinger, LLC. It performs simulations in the framework of classical mechanics, also termed ''molecular mechanics'', and can perform molecular dynamics simulations to model systems at finite temperatures using stochastic dynamics and mixed Monte Carlo algorithms. ''MacroModel'' supports Windows, Linux, macOS, Silicon Graphics (SGI) IRIX, and IBM AIX AIX (Advanced Interactive eXecutive, pronounced , "ay-eye-ex") is a series of proprietary Unix operating systems developed and sold by IBM for several of its computer platforms. Background Originally released for the IBM RT PC RISC .... The Macromodel software package was first been described in the scientific literature in 1990, and has b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Abalone (molecular Mechanics)
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field. Key features * 3D molecular graphics Automatic Force Field generator for bioelements: H, C, N, O* Building and editing chemical structures * Library of building blocks * Force fields: Assisted Model Building with Energy Refinement (AMBER) 94, 96, 99SB, 03; Optimized Potentials for Liquid Simulations (OPLS) * Geometry optimizing * Molecular dynamics with multiple time step integrator * Hybrid Monte Carlo * Replica exchange * Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ionic Liquid
An ionic liquid (IL) is a salt in the liquid state. In some contexts, the term has been restricted to salts whose melting point is below a specific temperature, such as . While ordinary liquids such as water and gasoline are predominantly made of electrically neutral molecules, ionic liquids are largely made of ions. These substances are variously called liquid electrolytes, ionic melts, ionic fluids, fused salts, liquid salts, or ionic glasses. Ionic liquids have many potential applications. They are powerful solvents and can be used as electrolytes. Salts that are liquid at near-ambient temperature are important for electric battery applications, and have been considered as sealants due to their very low vapor pressure. Any salt that melts without decomposing or vaporizing usually yields an ionic liquid. Sodium chloride (NaCl), for example, melts at into a liquid that consists largely of sodium cations () and chloride anions (). Conversely, when an ionic liquid is cooled, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BOSS (molecular Mechanics)
Boss may refer to: Occupations * Supervisor, often referred to as boss * Air boss, more formally, air officer, the person in charge of aircraft operations on an aircraft carrier * Crime boss, the head of a criminal organization * Fire boss, a person in charge of mine safety * Pit boss, the person who looks after the employees who work in a casino pit * Political boss, a person who controls a political region or constituency Places United States * Boss, Missouri, an unincorporated community * Boss, Texas, an unincorporated community * Bosstown, Wisconsin, an unincorporated community Moon * Boss (crater), a lunar crater People As a real name *Boss (surname) *Boss Mustapha, politician, Secretary of Nigerian government As a nickname or stage name Athletes * Lance Armstrong ("", born 1971), former professional cyclist * Sasha Banks (born 1992), American professional wrestler * Tomás Boy ("", born 1952), former Mexican professional football player and current coach * Bobby ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polyelectrolyte
Polyelectrolytes are polymers whose repeating units bear an electrolyte group. Ion#Anions and cations, Polycations and polyanions are polyelectrolytes. These groups dissociation (chemistry), dissociate in aqueous solutions (water), making the polymers charge (physics), charged. Polyelectrolyte properties are thus similar to both electrolytes (salts) and polymers (high molecular weight compounds) and are sometimes called polysalts. Like salts, their solutions are electrically conductive. Like polymers, their solutions are often viscosity, viscous. Charged molecular chains, commonly present in soft matter systems, play a fundamental role in determining structure, stability and the interactions of various molecular assemblies. Theoretical approaches to describing their statistical properties differ profoundly from those of their electrically neutral counterparts, while technological and industrial fields exploit their unique properties. Many biological molecules are polyelectrolytes. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA. Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and make up the genetic material. Nucleic acids are found in abundance in all living things, where they create, encode, and then store information of every living cell of every life-form on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded information is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Model
A molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected. The electronic structure is often also omitted unless it is necessary in illustrating the function of the molecule being modeled. Molecular models may be created for several reasons – as pedagogic tools for students or those unfamiliar with atomistic structures; as objects to generate or test theories (e.g., the structure of DNA); as analogue computers (e.g., for measuring distances and angles in flexible systems); or as a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graphical User Interface
The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, instead of text-based UIs, typed command labels or text navigation. GUIs were introduced in reaction to the perceived steep learning curve of CLIs ( command-line interfaces), which require commands to be typed on a computer keyboard. The actions in a GUI are usually performed through direct manipulation of the graphical elements. Beyond computers, GUIs are used in many handheld mobile devices such as MP3 players, portable media players, gaming devices, smartphones and smaller household, office and industrial controls. The term ''GUI'' tends not to be applied to other lower-display resolution types of interfaces, such as video games (where HUD (''head-up display'') is preferred), or not including flat screens like volumetric displays because ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
