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BranniganLab / density_threshold_affinity

Scripts to Assist Density Threshold Affinity Analysis - a method for obtaining free energies of protein-lipid binding. Originally described in: https://pubs.aip.org/aip/jcp/article/154/18/185102/200265/Spontaneous-lipid-binding-to-the-nicotinic and subsequently refined in: https://doi.org/10.1016/bs.mie.2024.03.008
https://doi.org/10.1016/bs.mie.2024.03.008
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Single-replica handling and multi-replica handling need to be defined #64

Open JesseSandberg opened 2 months ago

JesseSandberg commented 2 months ago

Currently multi-replica handling is the default, which isn't the most common use case. Current implementation is also hard-coded to a file structure that isn't necessary. Related to issue #56

JesseSandberg commented 2 months ago

There is also a logical difference between the multiple sites contained in a symmetric site and the multiple sites contained across replicas that may or may not need to be borne out in future code