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choderalab / feflow

Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
MIT License
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NEq cycling rebase #4

Closed ijpulidos closed 9 months ago

ijpulidos commented 9 months ago

This set of changes aim to rebase the NonEquilibriumCyclingProtocol to use the openfe objects in order to have a common code base for both protocols (openfe and neq cycling).

A significant portion of the settings and code for creating the individual OpenMM topologies and systems should be able to be shared between both protocols, as well as the creation of the creation of the Hybrid Topology.

Resolves #1

dotsdl commented 9 months ago

Awesome @ijpulidos! Excited for this!

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ijpulidos commented 9 months ago

@dotsdl I think this one should be ready to go to start working on optimizing the DAG units and thinking about what components migrate to openmmtools that should be shared between different protocols. Those changes I think are more suited for future iterations/PRs.