Fix grem, temper/grem, MSD


I have used " fix grem" and “temper/grem” to do the generalized replica exchange method in my system!
Since the dump files created by the fix “grem” contain continuous trajectories and require post-processing to obtain per-replica information, I used the python file from the tools/replica directory of LAMMPS for this purpose!
Now, I want to calculate the mean square displacement for each replica by rerun command!
Simply just using “fix MSD” and “rerun” commands can not give me the appropriate answer! and it is sth like this:


the X-direction is time and the Y-direction is the MSD!
Can you please let me know how to manage this issue?!

If you do a parallel tempering simulation, your time axis has no meaning anymore. Thus computing self-diffusion also is meaningless.

The reconstructed per-temperature trajectories will be disjointed after every swap, anyway, since they originate from different simulation instances.