Related to the discussion here, it is currently not possible to merge a water molecule with an ion since the RMSD alignment fails due to there not being enough degrees of freedom. In this case, we should skip the alignment and return an RMSD score of zero for the mapping. This will be useful for creating alchemical waters for use with SOMD2.
Related to the discussion here, it is currently not possible to merge a water molecule with an ion since the RMSD alignment fails due to there not being enough degrees of freedom. In this case, we should skip the alignment and return an RMSD score of zero for the mapping. This will be useful for creating alchemical waters for use with SOMD2.