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coarse-graining / cgnet

learning coarse-grained force fields
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Feature definition bonds vs distances #183

Closed psolsson closed 4 years ago

psolsson commented 4 years ago

How do you distinguish between bonds and distances in the features? What is the optimal use? Any why are they both necessary?

brookehus commented 4 years ago

Good question! The specification of certain contact pairs as bonds is purely for convenience and is not necessary for any functioning. When bonds are specified, the GeometryStatistics object can return lists of bond pair indices which can be input into e.g. a harmonic prior. The statistics functionalities also give you the opportunity to input consecutive backbone bead indices, and bonds between consecutive beads along that specified backbone can be automatically generated. Again, this is only for convenience.