GROMACS version: 2020.3
GROMACS modification: No
According to the manual http://manual.gromacs.org/documentation/current/onlinehelp/gmx-msd.html#gmx-msd, the diffusion constant is computed through a linear regression of MSD versus lag time. To verify that I had understood it correctly, I did the linear regression using both gnuplot and statsmodels (python package), and I got the same value as printed by gmx msd.
My question concerns the error estimation. In the description of the gmx msd command it says:
An error estimate given, which is the difference of the diffusion coefficients obtained from fits over the two halves of the fit interval.
Why is this a better error estimate than using the standard error of the regression coefficient?
Thanks for your help.