fix hardcoded distances, pbc and indexing in reaction loops
fix hardcoded distances, pbc and indexing in reaction loops

pdebuyl/RMPCDMD,pdebuyl-lab/RMPCDMD,laurensdeprez/RMPCDMD,pdebuyl-lab/RMPCDMD,pdebuyl/RMPCDMD,laurensdeprez/RMPCDMD