Align the snapshots to a reference structure: (1) the entire protein, (2) the most 'rigid' part of the protein, (3) the loop. For each of the alignments, measure the distances between the COM in the reference structure and in the snapshots. Comparing the results based on different alignments will allow you to filter out, if you want, the contributions from global and loop motions to the local mobility of the residue of interest.

Dear Martin and Esam, thank you for the answers. I have already tried using the PyMoL distance tool, and I do record a distance shift between different snapshots from the trajectory (dt 10ns).

However, please allow me to rephrase, I want to calculate the distance shift more often (lets say every 10 ps) in the trajectory to get an idea of something like distance vs time as a plot.

Thanks

Pallab, if you want to do the measurement every 10 ps, and if you know Python a little bit, you don't need PyMOL: write "for snapshot in snapshots" loop to go through your list of snapshots.

RMSF or RMSD per a certain residue will show You shifts of CA atoms (or it can be changed) in nm. Another way is rmsdist function..

Each MM-MD software has a different set of commands to perform the task at hand. If you are not knowledgeable with the software you are using to generate the MD trajectories, then save the frames and generate a script to measure the distances, as advised by others

make an index file and add annotation for distance calculation

Dear Martin, thanks for the idea. I won't admit to being fluent in Python, but, let me give that a try ;) Thanks....

Dear Alex, it was quite dumb of me (now that I think about it) to not create an index for the residue and then check the RMSD. Just didn't cross my mind. Let me give that a try. Thanks a lot. Cheers