[gmx-users] The difference between selecting residue groups with r (residue) or ri (residue index) under gmx make_ndx

[Johnny Tam]

Dear GROMACS staff,

Thank you very much for reading this email.

I have a question on the selection of residue groups when I use gmx
make_ndx:

What is the *difference *between selecting residues with *r (residue) or ri
(residue index)*?

Since the number of atoms after the selection differs between using r or
ri, I want to know what is the exact meaning of r and ri.

Using ri (residue index) gave me a number of atoms *closer* to the actual
number of atoms of the residues within that group when I counted
independently, compared with using r (residue).

Thank you very much and I look forward to your reply.

Best regards,
Tam