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Several sets of OPLS parameters have been published. There is OPLS-ua (united atom), which includes hydrogen atoms next to carbon implicitly in the carbon parameters, and can be used to save simulation time. OPLS-aa (all atom) includes every atom explicitly.
Structures up to ten thousands of atoms can be analyzed on a workstation, and up to a billion atoms using supercomputing. Examples include properties of metals and alloys, [ 22 ] [ 23 ] mineral-organic interfaces, [ 24 ] protein- and DNA-nanomaterial interactions, [ 25 ] earth and building materials, carbon nanostructures, batteries, and ...
The manipulation of atoms using optical fields is a vital and fundamental area of research within the field of atomic physics. This research revolves around leveraging the distinct characteristics of laser light and coherent optical fields to achieve precise control over various aspects of atomic systems.
Part of force field of ethane for the C-C stretching bond. In the context of chemistry, molecular physics, physical chemistry, and molecular modelling, a force field is a computational model that is used to describe the forces between atoms (or collections of atoms) within molecules or between molecules as well as in crystals.
SMILES generation algorithm for ciprofloxacin: break cycles, then write as branches off a main backbone. The Simplified Molecular Input Line Entry System (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings.
SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is an original method and its computer program implementation, to efficiently perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
Biochemical and Organic Simulation System (BOSS) is a general-purpose molecular modeling program that performs molecular mechanics calculations, Metropolis Monte Carlo statistical mechanics simulations, and semiempirical Austin Model 1 (AM1), PM3, and PDDG/PM3 quantum mechanics calculations. [1]
A mnemonic is a memory aid used to improve long-term memory and make the process of consolidation easier. Many chemistry aspects, rules, names of compounds, sequences of elements, their reactivity, etc., can be easily and efficiently memorized with the help of mnemonics.