At first, thanks for turning to me for help. If you want to do personal academic communication, you’d better to do it professionally, such as showing your institute, using the institute email address. Otherwise, you can post your questions in the mail list and a lot of expert can help you out, not just me. You will get the help sooner in this way.
Actually I haven’t worked on nanoindentation ever, maybe later. I just use LAMMPS and had a comment on LAMMPS problem. I haven’t ever use “centro/atom” command, but I doubt that the feasibility of your idea “make VMD to show me only the second group as type 2 and this way i can see dislocations which are moving”. What format do you dump? I feel that VMD won’t explain your specific column, not mention displaying based on it. I expect other people in the mail list will help you out.