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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. Proprietary: Schrödinger: MAPS [4] Yes Yes Yes Yes Yes Yes Yes No Yes
Most commonly, by writing the constituent B, C, N, O, P and S atoms in lower-case forms b, c, n, o, p and s, respectively. In the latter case, bonds between two aromatic atoms are assumed (if not explicitly shown) to be aromatic bonds. Thus, benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1.
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The total Coulomb energy is a sum over all pairwise combinations of atoms and usually excludes 1, 2 bonded atoms, 1, 3 bonded atoms, as well as 1, 4 bonded atoms [clarify]. [ 10 ] [ 11 ] [ 12 ] Atomic charges can make dominant contributions to the potential energy, especially for polar molecules and ionic compounds, and are critical to simulate ...
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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]