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47 lines
1.5 KiB
ReStructuredText
47 lines
1.5 KiB
ReStructuredText
OpenMM Absolute Binding Free Energy Protocol
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============================================
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.. _afe binding protocol api:
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This section provides details about the OpenMM Absolute Binding Free Energy Protocol
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implemented in OpenFE.
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Protocol API specification
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--------------------------
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.. module:: openfe.protocols.openmm_afe.equil_binding_afe_method
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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AbsoluteBindingProtocol
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ABFEComplexAnalysisUnit
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ABFEComplexSetupUnit
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ABFEComplexSimUnit
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ABFESolventAnalysisUnit
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ABFESolventSetupUnit
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ABFESolventSimUnit
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AbsoluteBindingProtocolResult
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Protocol Settings
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-----------------
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Below are the settings which can be tweaked in the protocol. The default settings (accessed using :meth:`AbsoluteBindingProtocol.default_settings`) will automatically populate settings which we have found to be useful for running binding free energy calculations. There will however be some cases (such as when calculating difficult to converge systems) where you will need to tweak some of the following settings.
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.. module:: openfe.protocols.openmm_afe.equil_afe_settings
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.. autopydantic_model:: AbsoluteBindingSettings
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:model-show-json: False
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:model-show-field-summary: False
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:model-show-config-member: False
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:model-show-config-summary: False
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:model-show-validator-members: False
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:model-show-validator-summary: False
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:field-list-validators: False
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:inherited-members: SettingsBaseModel
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:exclude-members: get_defaults
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:member-order: bysource
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