I want to compute the mean square displacement (MSD) of the center-of-mass of polymer. One case, computing MSD of center-of-mass of one polymer chain. Another case, computing MSD of center-of-mass of two or more polymer chains. How to realize it with lammps? And which commands should been used to compute the MSD of center-of-mass?
i would just pick a single atom near the center of your chain. since MSD makes the most sense in the long time limit, the motion of that atom is going to become increasingly similar to that of the center of mass.
Or you could use a combination of the 'msd' and 'reduce' computes.