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Explicit Water Model
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called ''site'', (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects. An alternative to the explicit water models is to use an implicit solvation model, also termed a continuum model, an example of which would be the COSMO solvation model or the polarizable continuum model (PCM) or a hybrid solvation model. Simple water models The rigid models are considered the simplest water models and rely on non-bonded interactions. In these models, bonding interactions are i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Water Models
Water (chemical formula ) is an inorganic, transparent, tasteless, odorless, and nearly colorless chemical substance, which is the main constituent of Earth's hydrosphere and the fluids of all known living organisms (in which it acts as a solvent). It is vital for all known forms of life, despite not providing food, energy or organic micronutrients. Its chemical formula, H2O, indicates that each of its molecules contains one oxygen and two hydrogen atoms, connected by covalent bonds. The hydrogen atoms are attached to the oxygen atom at an angle of 104.45°. "Water" is also the name of the liquid state of H2O at standard temperature and pressure. A number of natural states of water exist. It forms precipitation in the form of rain and aerosols in the form of fog. Clouds consist of suspended droplets of water and ice, its solid state. When finely divided, crystalline ice may precipitate in the form of snow. The gaseous state of water is steam or water vapor. Water co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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 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 structure and the force field * ''tranal' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Physical Chemistry A
''The Journal of Physical Chemistry A'' is a scientific journal which reports research on the chemistry of molecules - including their dynamics, spectroscopy, kinetics, structure, bonding, and quantum chemistry. It is published weekly by the American Chemical Society. Before 1997 the title was simply ''Journal of Physical Chemistry''. Owing to the ever-growing amount of research in the area, in 1997 the journal was split into ''Journal of Physical Chemistry A'' (molecular theoretical and experimental physical chemistry) and '' The Journal of Physical Chemistry B'' (solid state, soft matter, liquids, etc.). Beginning in 2007, the latter underwent a further split, with ''The Journal of Physical Chemistry C'' now being dedicated to nanotechnology, molecular electronics, and related subjects. Editors-in-chief *1896–1932 Wilder Dwight Bancroft, Joseph E. Trevor *1933–1951 S. C. Lind *1952–1964 William A. Noyes *1965–1969 F. T. Wall *1970–1980 Bryce Crawford *1980 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dielectric Permittivity
In electromagnetism, the absolute permittivity, often simply called permittivity and denoted by the Greek letter ''ε'' ( epsilon), is a measure of the electric polarizability of a dielectric. A material with high permittivity polarizes more in response to an applied electric field than a material with low permittivity, thereby storing more energy in the material. In electrostatics, the permittivity plays an important role in determining the capacitance of a capacitor. In the simplest case, the electric displacement field D resulting from an applied electric field E is :\mathbf = \varepsilon \mathbf. More generally, the permittivity is a thermodynamic function of state. It can depend on the frequency, magnitude, and direction of the applied field. The SI unit for permittivity is farad per meter (F/m). The permittivity is often represented by the relative permittivity ''ε''r which is the ratio of the absolute permittivity ''ε'' and the vacuum permittivity ''ε''0 :\ka ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Density
Density (volumetric mass density or specific mass) is the substance's mass per unit of volume. The symbol most often used for density is ''ρ'' (the lower case Greek letter rho), although the Latin letter ''D'' can also be used. Mathematically, density is defined as mass divided by volume: : \rho = \frac where ''ρ'' is the density, ''m'' is the mass, and ''V'' is the volume. In some cases (for instance, in the United States oil and gas industry), density is loosely defined as its weight per unit volume, although this is scientifically inaccurate – this quantity is more specifically called specific weight. For a pure substance the density has the same numerical value as its mass concentration. Different materials usually have different densities, and density may be relevant to buoyancy, purity and packaging. Osmium and iridium are the densest known elements at standard conditions for temperature and pressure. To simplify comparisons of density across different s ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polarization Density
In classical electromagnetism, polarization density (or electric polarization, or simply polarization) is the vector field that expresses the density of permanent or induced electric dipole moments in a dielectric material. When a dielectric is placed in an external electric field, its molecules gain electric dipole moment and the dielectric is said to be polarized. The electric dipole moment induced per unit volume of the dielectric material is called the electric polarization of the dielectric.''Introduction to Electrodynamics'' (3rd Edition), D.J. Griffiths, Pearson Education, Dorling Kindersley, 2007, ''McGraw Hill Encyclopaedia of Physics'' (2nd Edition), C.B. Parker, 1994, Polarization density also describes how a material responds to an applied electric field as well as the way the material changes the electric field, and can be used to calculate the forces that result from those interactions. It can be compared to magnetization, which is the measure of the corresponding ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Physical Chemistry
''The Journal of Physical Chemistry A'' is a scientific journal which reports research on the chemistry of molecules - including their dynamics, spectroscopy, kinetics, structure, bonding, and quantum chemistry. It is published weekly by the American Chemical Society. Before 1997 the title was simply ''Journal of Physical Chemistry''. Owing to the ever-growing amount of research in the area, in 1997 the journal was split into ''Journal of Physical Chemistry A'' (molecular theoretical and experimental physical chemistry) and ''The Journal of Physical Chemistry B'' (solid state, soft matter, liquids, etc.). Beginning in 2007, the latter underwent a further split, with ''The Journal of Physical Chemistry C'' now being dedicated to nanotechnology, molecular electronics, and related subjects. Editors-in-chief *1896–1932 Wilder Dwight Bancroft, Joseph E. Trevor *1933–1951 S. C. Lind *1952–1964 William A. Noyes *1965–1969 F. T. Wall *1970–1980 Bryce Crawford *1980–2004 Mos ... [...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. Furthermore ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Farad
The farad (symbol: F) is the unit of electrical capacitance, the ability of a body to store an electrical charge, in the International System of Units (SI). It is named after the English physicist Michael Faraday (1791–1867). In SI base units 1 F = 1 kg−1⋅ m−2⋅ s4⋅ A2. Definition The capacitance of a capacitor is one farad when one coulomb of charge changes the potential between the plates by one volt. Equally, one farad can be described as the capacitance which stores a one-coulomb charge across a potential difference of one volt. The relationship between capacitance, charge, and potential difference is linear. For example, if the potential difference across a capacitor is halved, the quantity of charge stored by that capacitor will also be halved. For most applications, the farad is an impractically large unit of capacitance. Most electrical and electronic applications are covered by the following SI prefixes: *1 mF (millifarad, one thousandth ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polarizability
Polarizability usually refers to the tendency of matter, when subjected to an electric field, to acquire an electric dipole moment in proportion to that applied field. It is a property of all matter, considering that matter is made up of elementary particles which have an electric charge, namely protons and electrons. When subject to an electric field, the negatively charged electrons and positively charged atomic nuclei are subject to opposite forces and undergo charge separation. Polarizability is responsible for a material's dielectric constant and, at high (optical) frequencies, its refractive index. The polarizability of an atom or molecule is defined as the ratio of its induced dipole moment to the local electric field; in a crystalline solid, one considers the dipole moment per unit cell. Note that the local electric field seen by a molecule is generally different from the macroscopic electric field that would be measured externally. This discrepancy is taken into account b ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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