Hello, I used the GMX msd -type Z option to calculate the results as shown in figure. I would like to ask how the figure"D [ resname > 1.75] = 0.3775(+/-0.4572)(1e-5 cm ^ 2/s)" is calculated. My X axis is 0-5000 and my y axis is about 0-4.7. The slope is about 4.7 over 5000, which is not close to 0.3775. Thank you.
The calculation process is documented within the tool itself. If you didn’t change any particular flag, GROMACS discards 20% of the MSD data (first and last 10%) and takes the linear fit of the remaining. The error is calculated as the difference between the fit executed on the two regions of the MSD plot.
You should check the linearity of the MSD in that region to see whether the application of the MSD formula has any meaning. You have quite a large error, it may be that the linearity is not respected at all.
