supporting OpenMM-ML about openfe HOT 3 CLOSED

I know this isn't supported, but any guidance on how to go about this? Any precaultions ?

That will "just work" if we add OpenMM-ML support to https://github.com/openmm/openmmforcefields -- which I haven't looked into, but before doing that I would just hack apart the protocol and see if you can get a system parameterized with openmm-ml to run, that should be around here (if you ignore partial charge assignment) https://github.com/OpenFreeEnergy/openfe/blob/main/openfe/protocols/openmm_rfe/equil_rfe_methods.py#L740

As of now this isn't something on our roadmap so we can't support it or devote time to it, but I am happy to provide some pointers and advice if you want to try and hack this in, I would aim first for a proof-of-concept before trying to do it The Right Way ™️

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Unfortunately from a scientific standpoint, this won't work (for alchemical transformations) - even if the code was made to allow it (which would require large changes to the hybrid topology factory too).

Very briefly, the main issue is that ML potentials, such as ANI, do not have a defined functional form that can be decoupled in the same way that classical FFs can. There are means to go around this, either through approaches such as AToM or the work of Rufa et al., but none that would work "today" in OpenFE.

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@mikemhenry Thank you for the pointers,
My initial thought was creating mixedSystem using OpenMM-ML and was trying to understand:

# openmmforcefields/generators/system_generators.py
class SystemGenerator:
    def create_system(...)
    ...
        # Build the System
        system = self.forcefield.createSystem(topology, **forcefield_kwargs)

        # Modify other forces as requested
        self._modify_forces(system)
    ...

# openfe/protocols/openmm_rfe/equil_rfe_methods.py    
class RelativeHybridTopologyProtocolUnit(gufe.ProtocolUnit):
    def run(...):
        # c. force the creation of parameters
            system_generator.create_system
        # create state A
            system_generator.create_system
        # create state B
            system_generator.create_system

how multiple calls to system_generator.create_system would interact with a mixedSystem.

Next I was going to look deeper into FF and system implementations but,

Unfortunately from a scientific standpoint, this won't work (for alchemical transformations)

@IAlibay thank you - saved me from heading in the wrong direction. I will take a look at AToM

closing this case for now.

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