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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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Allow passing a `json` file for forcefield parameters cache #50

Open ijpulidos opened 1 week ago

ijpulidos commented 1 week ago

The system generator allows for passing a json file with precomputed forcefield parameters for different molecules. We should make changes such as if the user specifies a cache file it gets copied to the corresponding shared/scratch directories and used from there. As of this moment, the protocol accepts the settings but does not copy any file to the shared/scratch directories.

This would avoid having to always compute the partial charges with some implementation, especially if users want to force a specific partial charges calculation.

IAlibay commented 1 week ago

As discussed by DM - this is, in my opinion, not the right solution to this problem. The preffered approach is user charges (as per https://docs.openfree.energy/en/stable/cookbook/user_charges.html) or assigning ffxml parameters directly through OpenMMSystemGenerationFFSettings.