plumed2
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Compute minimum distance from an image
This is something proposed on the mailing list. It's not so difficult to implement. Having the possibility to bias it would give a way to avoid interactions with periodic images in cases where a molecule can significantly change its shape.
Gromacs does something similar with gmx mindist -pi. Notice that gromacs can only do it for analysis (no bias).
Just to mention that this was mentioned as a possibly useful features at CECAM 2023 event.