Hi Marvin! The best way to do what you want is to create 1 pdb frame of the trajectory for your simulation box. Then open it with some text editor, like gedit and label the parts of your protein manually which you are interested to monitor. Then you run make_ndx command over that edited pdb-file and you can simply specify what you want. Also you can try to run make_ndx command over non-edited pdb file for your protein. In pdb file all residues are described better than in other files: it specifies the chains explicitly.

Hello Inna Ermilova , will try it. Thank you very much for your suggestion!

Hi,

Try this:

gmx distance -f md.xtc -s md.tpr -oall dist_filename.xvg -n index.ndx -select 'com of group "atom1" plus com of group "atom2"' -tu ns