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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] |
Force Field (chemistry)
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates. ''All-atom'' force fields provide parameters for every type of atom in ... [...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] |
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 imp ... [...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] |
Accelrys
BIOVIA is a software company headquartered in the United States, with representation in Europe and Asia. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries. Previously named Accelrys, it is a wholly owned subsidiary of Dassault Systèmes after an April 2014 acquisition and has been renamed BIOVIA. History Accelrys was formed in 2001 as a wholly owned subsidiary of Pharmacopeia, Inc. from the fusion of five companies: Molecular Simulations Inc., Synopsys Scientific Systems, Oxford Molecular, the Genetics Computer Group (GCG), and Synomics Ltd. MSI, itself a result of the combination of Biodesign, Cambridge Molecular Design, Polygen and, later, Biocad and Biosym Technologies. In late 2003, Pharmacopeia, Inc. separated its drug discovery and software development businesses. The drug discovery company retained the name Pharmacopeia and remained in Princeton ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' representation in which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free Energy Perturbation
Free energy perturbation (FEP) is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by Robert W. Zwanzig in 1954. According to the free-energy perturbation method, the free energy difference for going from state A to state B is obtained from the following equation, known as the ''Zwanzig equation'': :\Delta F(\mathbf \rightarrow \mathbf) = F_\mathbf - F_\mathbf = -k_\mathrm T \ln \left \langle \exp \left ( - \frac \right ) \right \rangle _\mathbf where ''T'' is the temperature, ''k''B is Boltzmann's constant, and the angular brackets denote an average over a simulation run for state A. In practice, one runs a normal simulation for state A, but each time a new configuration is accepted, the energy for state B is also computed. The difference between states A and B may be in the atom types involved, in which case the Δ''F ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Implicit Solvent
Implicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes. The implicit solvation model is justified in liquids, where the potential of mean force can be applied to approximate the averaged behavior of many highly dynamic solvent molecules. However, the interfaces and the interiors of biological membranes or proteins can also be considered as media with specific solvation or dielectric properties. These media are not necessarily uniform, since their proper ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Martin Karplus
Martin Karplus (born March 15, 1930) is an Austrian and American theoretical chemist. He is the Director of the Biophysical Chemistry Laboratory, a joint laboratory between the French National Center for Scientific Research and the University of Strasbourg, France. He is also the Theodore William Richards Professor of Chemistry, emeritus at Harvard University. Karplus received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Arieh Warshel, for "the development of multiscale models for complex chemical systems". Early life Martin Karplus was born in Vienna, Austria. He was a child when his family fled from the Nazi-occupation in Austria a few days after the Anschluss in March 1938, spending several months in Zürich, Switzerland and La Baule, France before immigrating to the United States. Prior to their immigration to the United States, the family was known for being "an intellectual and successful secular Jewish family" in Vienna. His grandfather, Johann Pau ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nvidia
Nvidia CorporationOfficially written as NVIDIA and stylized in its logo as VIDIA with the lowercase "n" the same height as the uppercase "VIDIA"; formerly stylized as VIDIA with a large italicized lowercase "n" on products from the mid 1990s to early-mid 2000s. Though unofficial, second letter capitalization of NVIDIA, i.e. nVidia, may be found within enthusiast communities and publications. ( ) is an American multinational technology company incorporated in Delaware and based in Santa Clara, California. It is a software and fabless company which designs graphics processing units (GPUs), application programming interface (APIs) for data science and high-performance computing as well as system on a chip units (SoCs) for the mobile computing and automotive market. Nvidia is a global leader in artificial intelligence hardware and software. Its professional line of GPUs are used in workstations for applications in such fields as architecture, engineering and construction, media ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Unix-like
A Unix-like (sometimes referred to as UN*X or *nix) operating system is one that behaves in a manner similar to a Unix system, although not necessarily conforming to or being certified to any version of the Single UNIX Specification. A Unix-like application is one that behaves like the corresponding Unix command or shell. Although there are general philosophies for Unix design, there is no technical standard defining the term, and opinions can differ about the degree to which a particular operating system or application is Unix-like. Some well-known examples of Unix-like operating systems include Linux and BSD. These systems are often used on servers, as well as on personal computers and other devices. Many popular applications, such as the Apache web server and the Bash shell, are also designed to be used on Unix-like systems. One of the key features of Unix-like systems is their ability to support multiple users and processes simultaneously. This allows users to run multipl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of Michigan
, mottoeng = "Arts, Knowledge, Truth" , former_names = Catholepistemiad, or University of Michigania (1817–1821) , budget = $10.3 billion (2021) , endowment = $17 billion (2021)As of October 25, 2021. , president = Santa Ono , provost = Laurie McCauley , established = , type = Public research university , academic_affiliations = , students = 48,090 (2021) , undergrad = 31,329 (2021) , postgrad = 16,578 (2021) , administrative_staff = 18,986 (2014) , faculty = 6,771 (2014) , city = Ann Arbor , state = Michigan , country = United States , coor = , campus = Midsize City, Total: , including arboretum , colors = Maize & Blue , nickname = Wolverines , sporti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
