Class
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Description
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AnnealProtocol
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Annealing protocol - describes an annealing / dynamics simulation in general terms.
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AnnealProtocolStore
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Grouping of AnnealProtocols
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AnnealStage
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Annealing stage - one of several consecutive stges.
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EnergyTerm
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Energy term used in a protocol, with successive scaling factors, refPotentialTerms
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PotentialScale
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Restraint potential scaling
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RefPotentialTerm
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Reference Energy Potential term. Defines the shape of the potential function. May be a term in an existing potential function, or a restraint energy term. May be characterised by parameters. The precise interpretation generally requires reference to the application.
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RefTermParameter
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Parameter that characterises a RefPotentialTerm
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