As Martin says if you have the mouse pointer into the visualization box and you press 1, you can select an atom, the atom you want and many as you want of your system. If you press 2 you can select a bond, 3 an angle and 4 a dihedral angle. The information is also in Graphics> Labels, you have detail information for atom, bond, angle or dihedral. You can also graphic the change of a bond, angle or dihedral of a trajectory in the same window (Labels, I mean), in the Graph flap.
Hello everyone, thank you for helping me with this.
Martin and Florencia, I did exactly what you told me to do but instead of getting atom indices I am getting 1 everywhere. I am attaching the VMD image for you to see. Is it because I am creating the file from LAMMPS output as a data file from Tk Console in VMD?
Also, I have to select the atoms 1 by 1. Is there a way to drag mouse pointer over the whole system and select all the atoms at the same time?
I actually wanted to see only the indices of the atoms on the VMD image screen with the corresponding atom because I am calculating the bond stretching with LAMMPS and if would be extremely useful if I know the indices of the atoms on the VMD screen. By comparing the atom indices with VMD and comparing bond stretching data I can determine which bond is breaking.
It seems that VMD reads all atoms (or at least those you show labeled) as having atom name "cp" and belonging to molecule (or residue) with identifier "1" but no molecule (or residue) name . If this is not what you intended then compare the file format of your data file with any standard PDB file and make the necessary changes for VMD to recognize the atoms correctly.
As for selecting/labeling multiple atoms at once, it should be possible, .e.g., with this script: