The indices written in the ndx file are those read from the atom id field of the gro or pdb file. Atom id and index can be out of sync if the structure file is wrong or if there is to many atoms. In the last case, the atom id becomes larger than the field and the count restart at 1.
The indices written in the ndx file are those read from the atom id field of the gro or pdb file. Atom id and index can be out of sync if the structure file is wrong or if there is to many atoms. In the last case, the atom id becomes larger than the field and the count restart at 1.