[gmx-users] Calculation of RMSF

[Nicolas Cheron]

Dear all,

I am puzzled by the way RMSF are computed. For a given trajectory (nothing
fancy, just a regular protein):
(1) I have computed RMSF 5 times for two frames i.e. Frame 1/2, 3/4, 5/6,
7/8 and 9/10, each time using the same pdb reference (if I compute RMSF for
a single frame I sometimes have -nan, that's why I did it for couple of
frames)
(2) I have then computed RMSF for the 10 frames at the same time (1-10).

I would expect that the average of RMSF^2 for (1) would equal RMSF^2 for
(2), but that's not the case. To give you some numbers for 4 Calpha carbons:
Avg of case (1)         case (2)
0,000722                  0,001673
0,000417                  0,001197
0,000400                   0,001096
0,000768                   0,001910
It doesn't seem to be a rounding issue, neither a systematic difference.

Can anyone please help me understand these differences?

Thank you

Nicolas

PS: in case someone suggests that the problem may come from pbc because the
protein would be split in two, it is not the case, the protein is whole.