Dear LAMMPS users,
When I tried to compute MSD on a triclinic box, even though the triclinic factors very small, say: triclinic box = (0 0 0) to (81.5697 81.5696 81.5696) with tilt (0.0407848 0 0)
I found the curve of MSD_x vs time is reasonable: first increase rough linearly and then flatten, MSD_x = ~0.002 A^2
But the MSD_y and MSD_z are crazy large. Even when t = 0, MSD_y = 1108.24 A^2 and MSD_z = 1111, and their variation with time is smaller than 0.03 A^2. These are obviously unreasonable, could you tell me the possible reasons? Thanks in advance.
the commands for msd are below: (I’m calculating vibrational MSD, so set average yes)
fix 1 all nve
compute MSD all msd com yes average yes
fix out_msd all ave/time 1 1 1 c_MSD c_MSD c_MSD c_MSD file msd.dat