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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.
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 ...
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.
In the context of chemistry and molecular modelling, the Interface force field (IFF) is a force field for classical molecular simulations of atoms, molecules, and assemblies up to the large nanometer scale, covering compounds from across the periodic table. [1]
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.
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.
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.