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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.
OPLS-AA, MMFF, GBSA solvent model, conformational sampling, minimizing, MD. Includes the Maestro GUI which provides visualizing, molecule building, calculation setup, job launch and monitoring, project-level organizing of results, access to a suite of other modelling programs.
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.
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 ...
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.
OPLS AMBER CHARMM GAFF MMFF QVBMM UFF Comments Abalone: UA 94, 96, 99SB, 03, GS, ii, Automatic FF generator [1] No No No No UFF-Dreiding-like field For proteins, DNA, ligands AMBER: Yes Yes Via chamber tool since v11 Yes No No No Ascalaph Designer: UA 94, 99SB, 03 No No No No No Avogadro: No No No Yes 94, 94s No Yes Balloon: No No No No 94 No ...
The sample is typically dissolved in a suitable solvent (acids, water) to create a liquid solution. This ensures the analytes are present as free atoms, ready for absorption. For solid samples like ores or minerals, additional steps like grinding and digestion may be required to break down the matrix and liberate the analytes. Step 2 ...
A hydroxyl group, for example, can be both a hydrogen bond donor, and a hydrogen bond acceptor, and it would be impossible to treat this with one OH pseudo-atom. About half the atoms in a protein or nucleic acid are non-polar hydrogens, so the use of united atoms can provide a substantial savings in computer time.