Hi everyone,

I would like to ask for your help with a question I have about computing MSD from `compute msd`

and `compute msd/chunk`

. I have noticed that the result from `msd/chunk`

are significantly different from `msd`

. While `compute msd`

shows a liner relationship between timestep and MSD, `compute msd/chunk`

was expected to show a similar result because the system is uniform everywhere. However, I have observed strong tfluctuations in the MSD values of each chunk from `compute msd/chunk`

, and the maximum MSD values are much larger than those from `compute msd`

. I am wondering if there might be an error in my code that is causing these discrepancies. Thank you very much in advance for your help.

This is part of my code and results:

```
# define bins and compute for "compute msd/chunk"----------------------------
group O type 1
group Si type 2
group Al type 3
group Ca type 4
variable cx equal "(xhi+xlo)/2"
variable cy equal "(yhi+ylo)/2"
variable cz equal "(zhi+zlo)/2"
compute bins_O O chunk/atom bin/sphere ${cx} ${cy} ${cz} 10 50 40
compute bins_Si Si chunk/atom bin/sphere ${cx} ${cy} ${cz} 10 50 40
compute bins_Al Al chunk/atom bin/sphere ${cx} ${cy} ${cz} 10 50 40
compute bins_Ca Ca chunk/atom bin/sphere ${cx} ${cy} ${cz} 10 50 40
compute msd_O all msd/chunk bins_O
compute msd_Si all msd/chunk bins_Si
compute msd_Al all msd/chunk bins_Al
compute msd_Ca all msd/chunk bins_Ca
# define "compute msd"-------------------------------------------------------------
compute msd_all_O O msd
compute msd_all_Si Si msd
compute msd_all_Al Al msd
compute msd_all_Ca Ca msd
# run a simulation--------------------------------------------------------
reset_timestep 0
fix 1 all nve
fix 2 all ave/time 1 1 10 c_msd_O[4] c_msd_Si[4] c_msd_Al[4] c_msd_Ca[4] file msd_chunk_matrix.txt mode vector
fix 3 all ave/time 1 1 10 c_msd_all_O[4] c_msd_all_Si[4] c_msd_all_Al[4] c_msd_all_Ca[4] file msd_all_matrix.txt mode scalar
run 10000
```

This is the MSD of `compute msd`

, a liner relationship can be seen: