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• W2898021236 endingPage "6092" @default.
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• W2898021236 abstract "Traditional approaches to specifying a molecular mechanics force field encode all the information needed to assign force field parameters to a given molecule into a discrete set of atom types. This is equivalent to a representation consisting of a molecular graph comprising a set of vertices, which represent atoms labeled by atom type, and unlabeled edges, which represent chemical bonds. Bond stretch, angle bend, and dihedral parameters are then assigned by looking up bonded pairs, triplets, and quartets of atom types in parameter tables to assign valence terms and using the atom types themselves to assign nonbonded parameters. This approach, which we call indirect chemical perception because it operates on the intermediate graph of atom-typed nodes, creates a number of technical problems. For example, atom types must be sufficiently complex to encode all necessary information about the molecular environment, making it difficult to extend force fields encoded this way. Atom typing also results in a proliferation of redundant parameters applied to chemically equivalent classes of valence terms, needlessly increasing force field complexity. Here, we describe a new approach to assigning force field parameters via direct chemical perception. Rather than working through the intermediary of the atom-typed graph, direct chemical perception operates directly on the unmodified chemical graph of the molecule to assign parameters. In particular, parameters are assigned to each type of force field term (e.g., bond stretch, angle bend, torsion, and Lennard-Jones) based on standard chemical substructure queries implemented via the industry-standard SMARTS chemical perception language, using SMIRKS extensions that permit labeling of specific atoms within a chemical pattern. We use this to implement a new force field format, called the SMIRKS Native Open Force Field (SMIRNOFF) format. We demonstrate the power and generality of this approach using examples of specific molecules that pose problems for indirect chemical perception and construct and validate a minimalist yet very general force field, SMIRNOFF99Frosst. We find that a parameter definition file only ∼300 lines long provides coverage of all but <0.02% of a 5 million molecule drug-like test set. Despite its simplicity, the accuracy of SMIRNOFF99Frosst for small molecule hydration free energies and selected properties of pure organic liquids is similar to that of the General Amber Force Field, whose specification requires thousands of parameters. This force field provides a starting point for further optimization and refitting work to follow." @default.
• W2898021236 created "2018-10-26" @default.
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• W2898021236 date "2018-10-11" @default.
• W2898021236 modified "2023-10-09" @default.
• W2898021236 title "Escaping Atom Types in Force Fields Using Direct Chemical Perception" @default.
• W2898021236 cites W1031578623 @default.
• W2898021236 cites W185137928 @default.
• W2898021236 cites W1910508441 @default.
• W2898021236 cites W1911338432 @default.
• W2898021236 cites W1968755416 @default.
• W2898021236 cites W1976499671 @default.
• W2898021236 cites W2008505552 @default.
• W2898021236 cites W2009313526 @default.
• W2898021236 cites W2014060139 @default.
• W2898021236 cites W2015688756 @default.
• W2898021236 cites W2018518196 @default.
• W2898021236 cites W2019465613 @default.
• W2898021236 cites W2021827099 @default.
• W2898021236 cites W2024216557 @default.
• W2898021236 cites W2024762727 @default.
• W2898021236 cites W2027482274 @default.
• W2898021236 cites W2027639883 @default.
• W2898021236 cites W2037535298 @default.
• W2898021236 cites W2039588355 @default.
• W2898021236 cites W2048524630 @default.
• W2898021236 cites W2048541167 @default.
• W2898021236 cites W2051381895 @default.
• W2898021236 cites W2058938611 @default.
• W2898021236 cites W2064414576 @default.
• W2898021236 cites W2065837216 @default.
• W2898021236 cites W2072683434 @default.
• W2898021236 cites W2078374001 @default.
• W2898021236 cites W2087271871 @default.
• W2898021236 cites W2088542750 @default.
• W2898021236 cites W2090431249 @default.
• W2898021236 cites W2107136830 @default.
• W2898021236 cites W2110183365 @default.
• W2898021236 cites W2114227821 @default.
• W2898021236 cites W2114926916 @default.
• W2898021236 cites W2118233996 @default.
• W2898021236 cites W2122199548 @default.
• W2898021236 cites W2125034904 @default.
• W2898021236 cites W2128494768 @default.
• W2898021236 cites W2131288855 @default.
• W2898021236 cites W2132262459 @default.
• W2898021236 cites W2136141445 @default.
• W2898021236 cites W2137052779 @default.
• W2898021236 cites W2144288821 @default.
• W2898021236 cites W2147993766 @default.
• W2898021236 cites W2150981663 @default.
• W2898021236 cites W2153228625 @default.
• W2898021236 cites W2154449781 @default.
• W2898021236 cites W2155415467 @default.
• W2898021236 cites W2157599496 @default.
• W2898021236 cites W2159010139 @default.
• W2898021236 cites W2169678694 @default.
• W2898021236 cites W2170146596 @default.
• W2898021236 cites W2171268876 @default.
• W2898021236 cites W2171697771 @default.
• W2898021236 cites W2176516200 @default.
• W2898021236 cites W2222589778 @default.
• W2898021236 cites W2300061772 @default.
• W2898021236 cites W2317735345 @default.
• W2898021236 cites W2323439927 @default.
• W2898021236 cites W2404280981 @default.
• W2898021236 cites W2412116265 @default.
• W2898021236 cites W2475317853 @default.
• W2898021236 cites W2492804765 @default.
• W2898021236 cites W2510426927 @default.
• W2898021236 cites W2514249419 @default.
• W2898021236 cites W2523906298 @default.
• W2898021236 cites W2540491215 @default.
• W2898021236 cites W2560705618 @default.
• W2898021236 cites W2564264868 @default.
• W2898021236 cites W2566398673 @default.
• W2898021236 cites W2586213517 @default.
• W2898021236 cites W2589948472 @default.
• W2898021236 cites W2594183968 @default.
• W2898021236 cites W2595808071 @default.
• W2898021236 cites W2597025763 @default.
• W2898021236 cites W2619318203 @default.
• W2898021236 cites W2730519791 @default.
• W2898021236 cites W2790470680 @default.
• W2898021236 cites W2791904540 @default.
• W2898021236 cites W2903196289 @default.
• W2898021236 cites W2949223833 @default.

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