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OPLS
The OPLS (Optimized Potentials for Liquid Simulations) force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University. Functional form The functional form of the OPLS force field is very similar to that of AMBER: E \left(r^N \right ) = E_\mathrm + E_\mathrm + E_\mathrm + E_\mathrm E_\mathrm = \sum_\mathrm K_r (r-r_0)^2 \, E_\mathrm = \sum_\mathrm k_\theta (\theta-\theta_0)^2 \, E_\mathrm = \sum_\mathrm \left( \frac \left 1 + \cos (\phi-\phi_1) \right + \frac \left 1 - \cos (2\phi-\phi_2) \right + \frac \left 1 + \cos (3\phi-\phi_3) \right + \frac \left 1 - \cos (4\phi-\phi_4) \right \right) E_\mathrm = \sum_ f_ \left( \frac - \frac + \frac \right) with the combining rules A_ = \sqrt and C_ = \sqrt. Intramolecular nonbonded interactions E_\mathrm are counted only for atoms three or more bonds apart; 1,4 interactions are sca ... [...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] |
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] |
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] |
Force Fields
Force field may refer to: Science * Force field (chemistry), a set of parameter and equations for use in molecular mechanics simulations * Force field (physics), a vector field indicating the forces exerted by one object on another * Force field (technology), a barrier made up of energy, plasma or particles to protect a person, area or object from attacks or intrusions or as a means of containment or confinement * Force field, a region in the spinal cord that causes limbs to exert a consistent force depending on the limbs' position * Force-field analysis, a concept in the social sciences Arts and entertainment * ''Force Field'' (album), by the Atomic Bitchwax, 2017 * ''Forcefield'' (album), by Tokyo Police Club, 2014 * "Force Field", by Smash Mouth from ''Smash Mouth'' (album), 2001 * Forcefield (art collective), an American noise band and art collective * Forcefield (band), a British hard rock band * "Force Field", the theme tune of the British game show ''The Crystal Maze ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NAMD
Nanoscale Molecular Dynamics (NAMD, formerly Not Another Molecular Dynamics Program) is computer software for molecular dynamics simulation, written using the Charm++ parallel programming model. It is noted for its parallel efficiency and is often used to simulate large systems (millions of atoms). It has been developed by the collaboration of the Theoretical and Computational Biophysics Group (TCB) and the Parallel Programming Laboratory (PPL) at the University of Illinois at Urbana–Champaign. It was introduced in 1995 by Nelson ''et al.'' as a parallel molecular dynamics code enabling interactive simulation by linking to the visualization code VMD. NAMD has since matured, adding many features and scaling beyond 500,000 processor cores. NAMD has an interface to quantum chemistry packages ORCA and MOPAC, as well as a scripted interface to many other quantum packages. Together with Visual Molecular Dynamics (VMD) and QwikMD, NAMD's interface provides access to hybrid QM/MM simula ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LAMMPS
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics program from Sandia National Laboratories. LAMMPS makes use of Message Passing Interface (MPI) for parallel communication and is free and open-source software, distributed under the terms of the GNU General Public License. LAMMPS was originally developed under a Cooperative Research and Development Agreement (CRADA) between two laboratories from United States Department of Energy and three other laboratories from private sector firms. , it is maintained and distributed by researchers at the Sandia National Laboratories and Temple University. Features For computing efficiency, LAMMPS uses neighbor lists (Verlet lists) to keep track of nearby particles. The lists are optimized for systems with particles that repel at short distances, so that the local density of particles never grows too large. On parallel computers, LAMMPS uses spatial-decomposition techniques to partition the simulatio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
TINKER
Tinker or tinkerer is an archaic term for an itinerant tinsmith who mends household utensils. Description ''Tinker'' for metal-worker is attested from the thirteenth century as ''tyckner'' or ''tinkler''. Some travelling groups and Romani people specialised in the trade, and the name was particularly associated with indigenous Irish Travellers and Scottish Highland Travellers – the name of whose language '' Beurla Reagaird'' means "speech of the metalworkers".Kirk, J. & Ó Baoill, D. ''Travellers and their Language'' (2002) Queen's University Belfast However, this use is considered offensive. The term "tinker", in British English, may refer to a mischievous child. Some modern-day nomads with an English, an Irish or a Scottish influence call themselves "techno-tinkers" or "technogypsies" in a revival of sorts of the romantic view of the tinker's lifestyle. "Tinker's dam" or "damn" and "tinker's curse" Both phrases tinker's damn and tinker's curse can be applied to ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
William L
William is a male given name of Germanic origin.Hanks, Hardcastle and Hodges, ''Oxford Dictionary of First Names'', Oxford University Press, 2nd edition, , p. 276. It became very popular in the English language after the Norman conquest of England in 1066,All Things William"Meaning & Origin of the Name"/ref> and remained so throughout the Middle Ages and into the modern era. It is sometimes abbreviated "Wm." Shortened familiar versions in English include Will, Wills, Willy, Willie, Bill, and Billy. A common Irish form is Liam. Scottish diminutives include Wull, Willie or Wullie (as in Oor Wullie or the play ''Douglas''). Female forms are Willa, Willemina, Wilma and Wilhelmina. Etymology William is related to the given name ''Wilhelm'' (cf. Proto-Germanic ᚹᛁᛚᛃᚨᚺᛖᛚᛗᚨᛉ, ''*Wiljahelmaz'' > German ''Wilhelm'' and Old Norse ᚢᛁᛚᛋᛅᚼᛅᛚᛘᛅᛋ, ''Vilhjálmr''). By regular sound changes, the native, inherited English form of the name shoul ... [...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] |
