I know that g_msd calculates the D using the least square (LSQ) method.
But I dont know how to calculate the deviation of D. In this case, how
does g_msd get +/- 0.0366?

This snippet can be found by g_msd -h or on the online documentation:

An error estimate given, which is the difference of the diffusion coefficients obtained from fits over the two halfs of the fit interval.

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