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choderalab / perses

Experiments with expanded ensembles to explore chemical space
http://perses.readthedocs.io
MIT License
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REST max temperature from CLI #1195

Open ijpulidos opened 1 year ago

ijpulidos commented 1 year ago

Currently perses REST capabilities are not being used in the small molecule pipeline from CLI. One quick way to do this is passing a configuration option from the YAML file to be used as t_max when setting up the sampler in https://github.com/choderalab/perses/blob/53c61b8bfddd6f815d2e4523af5d8c77eba030d8/perses/app/setup_relative_calculation.py#L698

This would allow sampling using REST in the small molecule pipeline, which might be something that we would like to have and experiment with in the near future.

ijpulidos commented 1 year ago

We should do the same validation as we do with the other parameters here https://github.com/choderalab/perses/blob/53c61b8bfddd6f815d2e4523af5d8c77eba030d8/perses/app/setup_relative_calculation.py#L1076

zhang-ivy commented 1 year ago

We can write a test that checks that the rest lambda values are changing (and between 0 and 1) when we use T_max != 300 K. We can do this by checking state.lambda_rest_bonds where state is one of the non-endstate thermodynamic states (i.e. a state with lambda > 0 or < 1)..