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909d29ad25
* split md protocol to setup and simulate, add restart support * allow for resume in any stage * add a single run dynamics function * update restart to only look for checkpoints, split out remaining step logic, update tests --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
41 lines
897 B
ReStructuredText
41 lines
897 B
ReStructuredText
OpenMM Molecular Dynamics (MD) Protocol
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=======================================
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.. _md protocol api:
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A Protocol for running MD simulation using OpenMM.
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Protocol API Specification
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--------------------------
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.. module:: openfe.protocols.openmm_md
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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PlainMDProtocol
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PlainMDSetupUnit
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PlainMDSimulationUnit
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PlainMDProtocolResult
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Protocol Settings
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-----------------
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.. module:: openfe.protocols.openmm_md.plain_md_settings
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.. autopydantic_model:: PlainMDProtocolSettings
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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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