MSD simulations

Dear all,

I am trying to extract the MSD plot through the GUI code after a NPT simulation while the result shows a zigzag curve instead of the common linear relation with time. What I have done before was run a NVT equilibrium first and then copy the result to run a NPT equilibrium. My CONTROL file is posed as follows:

temperature 900 #900K
#zero #10K
pressure 0.001 # 1atm

ensemble npt hoover 1.0 1.5

timestep 0.0005 # 0.5 fs timestep
#timestep variable 0.002

#restart scale

steps 2.0E05
equilibration 2.0E04
scale 5
dump 100
trajectory 20 2000 0
integration velocity verlet

cutoff 10
ewald precision 1.0E-6
#densvar 8

print 2

stack 50
stats 10

job time 500000
close time 20


I have tried some ways, such as changing the timestep from 0.005ps to 0.0005ps and the thermostat and barostat relaxation times in ensemble while none could work well. Even if I took the example in the TES files as a test, the result was not good either.

I appreciate if anyone could give me some suggestions on this problem.