an assortment of codes that I used in/invented during my PhD including the qmmm water clustering code and the gmx mpqc interface code for gromacs 4.0.7
connectivity is called: void clusterAlgorithm(t_QMrec *qm,FILE *fpo) in https://github.com/richardtjornhammar/gmxhacks/blob/main/src/qmmm_code/src/mdlib/qm_cluster.c
FOR A DESCRIPTION READ PAGE 30 (16 INTERNAL NUMBERING) of: https://kth.diva-portal.org/smash/get/diva2:748464/FULLTEXT01.pdf
https://doi.org/10.1016/j.bpj.2009.12.224
The description of the code can be found in my PhD thesis